Rosetta 3.4
File List
Here is a list of all files with brief descriptions:
doc/apps/pilot/make_table_of_pilot_apps.py
doc/developer/example_protocol.cc
doc/developer/jd2_example.cc
src/core/init.ccOptions system initialization routines
src/core/init.hhCore Init functions
src/core/svn_version.cc
src/core/svn_version.hh
src/core/types.hhRosetta project type declarations
src/core/chemical/AA.ccTranslation between amino acid enum and string name/one letter char codes
src/core/chemical/AA.hh
src/core/chemical/Adduct.ccDefinition of residue adduct class
src/core/chemical/Adduct.fwd.hhDeclaration of class for adducts on residues
src/core/chemical/Adduct.hhDeclaration of implementation class for residue adducts
src/core/chemical/adduct_util.cc
src/core/chemical/adduct_util.hh
src/core/chemical/AtomICoor.ccDeclaration of implementation class for abstract class Residue
src/core/chemical/AtomICoor.fwd.hhDeclaration of implementation class for abstract class Residue
src/core/chemical/AtomICoor.hhDeclaration of implementation class for abstract class Residue
src/core/chemical/AtomType.cc
src/core/chemical/AtomType.fwd.hh
src/core/chemical/AtomType.hh
src/core/chemical/AtomTypeDatabaseIO.ccWrite chemical information associated with atom types to a database
src/core/chemical/AtomTypeDatabaseIO.fwd.hh
src/core/chemical/AtomTypeDatabaseIO.hh
src/core/chemical/AtomTypeSet.cc
src/core/chemical/AtomTypeSet.fwd.hh
src/core/chemical/AtomTypeSet.hh
src/core/chemical/automorphism.cc
src/core/chemical/automorphism.hh
src/core/chemical/ChemicalManager.ccChemical manager class
src/core/chemical/ChemicalManager.fwd.hh
src/core/chemical/ChemicalManager.hhChemical manager class header
src/core/chemical/CSDAtomType.hh
src/core/chemical/CSDAtomTypeSet.cc
src/core/chemical/CSDAtomTypeSet.fwd.hh
src/core/chemical/CSDAtomTypeSet.hh
src/core/chemical/Element.ccMolecular mechanics atom type class
src/core/chemical/Element.fwd.hh
src/core/chemical/Element.hhMolecular mechanics atom type class
src/core/chemical/ElementSet.cc
src/core/chemical/ElementSet.fwd.hh
src/core/chemical/ElementSet.hh
src/core/chemical/MMAtomType.ccMolecular mechanics atom type class
src/core/chemical/MMAtomType.fwd.hh
src/core/chemical/MMAtomType.hhMolecular mechanics atom type class
src/core/chemical/MMAtomTypeSet.cc
src/core/chemical/MMAtomTypeSet.fwd.hh
src/core/chemical/MMAtomTypeSet.hh
src/core/chemical/Patch.cc
src/core/chemical/Patch.fwd.hh
src/core/chemical/Patch.hh
src/core/chemical/PatchOperation.cc
src/core/chemical/PatchOperation.fwd.hh
src/core/chemical/PatchOperation.hh
src/core/chemical/ResConnID.cc
src/core/chemical/ResConnID.fwd.hh
src/core/chemical/ResConnID.hh
src/core/chemical/residue_io.cc
src/core/chemical/residue_io.hh
src/core/chemical/ResidueConnection.cc
src/core/chemical/ResidueConnection.fwd.hhDeclaration of implementation class for abstract class Residue
src/core/chemical/ResidueConnection.hhInter-residue chemical bond connection point class declaration
src/core/chemical/ResidueDatabaseIO.cc
src/core/chemical/ResidueDatabaseIO.fwd.hh
src/core/chemical/ResidueDatabaseIO.hh
src/core/chemical/ResidueSelector.cc
src/core/chemical/ResidueSelector.fwd.hh
src/core/chemical/ResidueSelector.hh
src/core/chemical/ResidueSupport.cc
src/core/chemical/ResidueSupport.hhSupport functions for class residue; functions that should not be included as part of the class
src/core/chemical/ResidueType.cc
src/core/chemical/ResidueType.fwd.hhDeclaration of implementation class for abstract class Residue
src/core/chemical/ResidueType.hh
src/core/chemical/ResidueTypeSet.cc
src/core/chemical/ResidueTypeSet.fwd.hh
src/core/chemical/ResidueTypeSet.hh
src/core/chemical/types.hh
src/core/chemical/util.ccUtilities for modifying and utilizing Residues and other core::chemical classes
src/core/chemical/util.hhUtilities for modifying and utilizing Residues and other core::chemical classes
src/core/chemical/VariantType.ccVariantTypes are used by Patches
src/core/chemical/VariantType.fwd.hh
src/core/chemical/VariantType.hh
src/core/chemical/orbitals/AssignOrbitals.cc
src/core/chemical/orbitals/AssignOrbitals.hh
src/core/chemical/orbitals/ICoorOrbitalData.cc
src/core/chemical/orbitals/ICoorOrbitalData.hh
src/core/chemical/orbitals/OrbitalType.cc
src/core/chemical/orbitals/OrbitalType.fwd.hh
src/core/chemical/orbitals/OrbitalType.hh
src/core/chemical/orbitals/OrbitalTypeMapper.cc
src/core/chemical/orbitals/OrbitalTypeMapper.fwd.hh
src/core/chemical/orbitals/OrbitalTypeMapper.hh
src/core/chemical/orbitals/OrbitalTypeSet.cc
src/core/chemical/orbitals/OrbitalTypeSet.fwd.hh
src/core/chemical/orbitals/OrbitalTypeSet.hh
src/core/chemical/rna/RNA_ResidueType.cc
src/core/chemical/rna/RNA_ResidueType.fwd.hh
src/core/chemical/rna/RNA_ResidueType.hh
src/core/chemical/sdf/ctab_base.cc
src/core/chemical/sdf/ctab_base.fwd.hh
src/core/chemical/sdf/ctab_base.hh
src/core/chemical/sdf/ctab_parser.cc
src/core/chemical/sdf/ctab_parser.fwd.hhForward declarations for ctab_parser
src/core/chemical/sdf/ctab_parser.hh
src/core/chemical/sdf/ctab_typer.cc
src/core/chemical/sdf/ctab_typer.fwd.hhForward declarations for ctab_typer
src/core/chemical/sdf/ctab_typer.hhDetermine the type of an atom
src/core/chemical/sdf/mol_parser.ccImplementation of molfile parser
src/core/chemical/sdf/mol_parser.fwd.hhForward declarations for molfile parser class
src/core/chemical/sdf/mol_parser.hhHeader file for molfile parser
src/core/chemical/sdf/mol_util.cc
src/core/chemical/sdf/mol_util.fwd.hh
src/core/chemical/sdf/mol_util.hh
src/core/chemical/sdf/mol_writer.cc
src/core/chemical/sdf/mol_writer.fwd.hh
src/core/chemical/sdf/mol_writer.hh
src/core/chemical/sdf/MolData.cc
src/core/chemical/sdf/MolData.fwd.hh
src/core/chemical/sdf/MolData.hh
src/core/chemical/sdf/sdf_parser.ccSdf file parser implementation
src/core/chemical/sdf/sdf_parser.fwd.hhForward declarations for sdf file parsing class
src/core/chemical/sdf/sdf_parser.hhSdf file parser header
src/core/chemical/sdf/v2_parser.cc
src/core/chemical/sdf/v2_parser.fwd.hh
src/core/chemical/sdf/v2_parser.hh
src/core/chemical/sdf/v3_parser.cc
src/core/chemical/sdf/v3_parser.fwd.hh
src/core/chemical/sdf/v3_parser.hh
src/core/coarse/Coarse.hh
src/core/coarse/CoarseEtable.cc
src/core/coarse/CoarseEtable.fwd.hh
src/core/coarse/CoarseEtable.hh
src/core/coarse/Rules.cc
src/core/coarse/Rules.fwd.hh
src/core/coarse/Rules.hh
src/core/coarse/Translator.cc
src/core/coarse/Translator.fwd.hh
src/core/coarse/Translator.hh
src/core/coarse/TranslatorSet.cc
src/core/coarse/TranslatorSet.fwd.hh
src/core/coarse/TranslatorSet.hh
src/core/conformation/AbstractRotamerTrie.fwd.hhForward declaration of the AbstractRotamerTrie class, defined in the conformation layer
src/core/conformation/AbstractRotamerTrie.hhBase class from which all Tries will derive; this class is a handle for the tries that will be defined in core/scoring, but which have to be stored by the RotamerSetBase class defined in core/conformation
src/core/conformation/Atom.fwd.hh
src/core/conformation/Atom.hh
src/core/conformation/AtomGraph.cc
src/core/conformation/AtomGraph.fwd.hh
src/core/conformation/AtomGraph.hh
src/core/conformation/AtomGraphData.fwd.hh
src/core/conformation/AtomGraphData.hh
src/core/conformation/Conformation.cc
src/core/conformation/Conformation.fwd.hhForward declaration for Conformation.hh
src/core/conformation/Conformation.hhConformation container
src/core/conformation/find_neighbors.fwd.hh
src/core/conformation/find_neighbors.hh
src/core/conformation/PointGraph.ccGraph for detecting neighbors; vertices store points, edges store square distances
src/core/conformation/PointGraph.fwd.hhGraph for detecting neighbors; vertices store points, edges store square distances
src/core/conformation/PointGraph.hhGraph for detecting neighbors; vertices store points, edges store square distances
src/core/conformation/PointGraphData.fwd.hh
src/core/conformation/PointGraphData.hhClasses to work with UpperEdgeGraph for fast neighbor detection
src/core/conformation/PseudoBond.cc
src/core/conformation/PseudoBond.fwd.hh
src/core/conformation/PseudoBond.hh
src/core/conformation/Residue.cc
src/core/conformation/Residue.functions.ccImplementation of non-member functions that operate on Residue objects
src/core/conformation/Residue.functions.hhHeader file for non-member functions that operate on Residue objects
src/core/conformation/Residue.fwd.hh
src/core/conformation/Residue.hh
src/core/conformation/ResidueFactory.cc
src/core/conformation/ResidueFactory.hh
src/core/conformation/ResidueKinWriter.ccClass to write kinemage-formatted output for Residue and Conformation
src/core/conformation/ResidueKinWriter.fwd.hh
src/core/conformation/ResidueKinWriter.hhClass to write kinemage-formatted output for Residue and Conformation
src/core/conformation/ResidueMatcher.cc
src/core/conformation/ResidueMatcher.fwd.hh
src/core/conformation/ResidueMatcher.hh
src/core/conformation/RotamerSetBase.ccRotamerSetBase class implementation
src/core/conformation/RotamerSetBase.fwd.hh
src/core/conformation/RotamerSetBase.hhAbstract base class for a class that holds disembodied Residues (ie not contained within a Pose) as Rotamers
src/core/conformation/RotamerSetCacheableDataType.hhEnum for the DataCache within the RotamerSet class; EnergyMethods in core/scoring forward-declare themselves here if they intend to cache data within the the RotamerSet
src/core/conformation/util.cc
src/core/conformation/util.hh
src/core/conformation/orbitals/OrbitalXYZCoords.cc
src/core/conformation/orbitals/OrbitalXYZCoords.hh
src/core/conformation/signals/ConnectionEvent.fwd.hhForward declaration for core::conformation::signals::ConnectionEvent
src/core/conformation/signals/ConnectionEvent.hhSignal a change in the connection with a Conformation object, e.g. destruction or transfer
src/core/conformation/signals/GeneralEvent.fwd.hhForward declaration for core::conformation::signals::GeneralEvent
src/core/conformation/signals/GeneralEvent.hhSignal for a general change in a Conformation
src/core/conformation/signals/IdentityEvent.fwd.hhForward declaration for core::conformation::signals::IdentityEvent
src/core/conformation/signals/IdentityEvent.hhSignal a residue identity change in a Conformation (e.g. residue identity change)
src/core/conformation/signals/LengthEvent.fwd.hhForward declaration for core::conformation::signals::LengthEvent
src/core/conformation/signals/LengthEvent.hhSignal for a change in length of residues in a Conformation
src/core/conformation/signals/XYZEvent.fwd.hhForward declaration for core::conformation::signals::XYZEvent
src/core/conformation/signals/XYZEvent.hhSignal for a change in XYZ coordinates in a Conformation
src/core/conformation/symmetry/SymDof.ccClass to store ingformation about symmetrical dofs
src/core/conformation/symmetry/SymDof.fwd.hh
src/core/conformation/symmetry/SymDof.hhSymDof data container
src/core/conformation/symmetry/SymmData.ccClass to store symmetry data specified from input files
src/core/conformation/symmetry/SymmData.fwd.hh
src/core/conformation/symmetry/SymmData.hhSymmetry data container
src/core/conformation/symmetry/SymmDataFactory.cc
src/core/conformation/symmetry/SymmDataFactory.hh
src/core/conformation/symmetry/SymmetricConformation.cc
src/core/conformation/symmetry/SymmetricConformation.fwd.hh
src/core/conformation/symmetry/SymmetricConformation.hhSymmetry conformation container
src/core/conformation/symmetry/SymmetryInfo.cc
src/core/conformation/symmetry/SymmetryInfo.fwd.hh
src/core/conformation/symmetry/SymmetryInfo.hh
src/core/conformation/symmetry/SymSlideInfo.ccClass to store ingformation about symmetrical dofs
src/core/conformation/symmetry/SymSlideInfo.fwd.hh
src/core/conformation/symmetry/SymSlideInfo.hhSymSlideInfo data container
src/core/conformation/symmetry/util.cc
src/core/conformation/symmetry/util.hhUtility functions for handling of symmetric conformations
src/core/conformation/symmetry/VirtualCoordinate.ccVirtualCoordinate container
src/core/conformation/symmetry/VirtualCoordinate.fwd.hh
src/core/conformation/symmetry/VirtualCoordinate.hh
src/core/conformation/symmetry/VirtualCoordinates.ccVirtualCoordinate container
src/core/conformation/symmetry/VirtualCoordinates.hh
src/core/fragment/BaseCacheUnit.hh
src/core/fragment/BBTorsionAndAnglesSRFD.cc
src/core/fragment/BBTorsionAndAnglesSRFD.hh
src/core/fragment/BBTorsionSRFD.cc
src/core/fragment/BBTorsionSRFD.fwd.hh
src/core/fragment/BBTorsionSRFD.hh
src/core/fragment/ConstantLengthFragSet.cc
src/core/fragment/ConstantLengthFragSet.fwd.hh
src/core/fragment/ConstantLengthFragSet.hh
src/core/fragment/ConstantLengthFragSetIterator_.hh
src/core/fragment/FragCache.fwd.hh
src/core/fragment/FragCache.hh
src/core/fragment/FragData.cc
src/core/fragment/FragData.fwd.hh
src/core/fragment/FragData.hh
src/core/fragment/FragID.cc
src/core/fragment/FragID.fwd.hh
src/core/fragment/FragID.hh
src/core/fragment/FragID_Iterator.cc
src/core/fragment/FragID_Iterator.fwd.hh
src/core/fragment/FragID_Iterator.hh
src/core/fragment/FragmentIO.cc
src/core/fragment/FragmentIO.hh
src/core/fragment/FragmentRmsd.cc
src/core/fragment/FragmentRmsd.fwd.hh
src/core/fragment/FragmentRmsd.hh
src/core/fragment/FragSet.cc
src/core/fragment/FragSet.fwd.hh
src/core/fragment/FragSet.hh
src/core/fragment/FragSetCollection.cc
src/core/fragment/FragSetCollection.fwd.hh
src/core/fragment/FragSetCollection.hh
src/core/fragment/Frame.cc
src/core/fragment/Frame.fwd.hh
src/core/fragment/Frame.hh
src/core/fragment/FrameIterator.cc
src/core/fragment/FrameIterator.fwd.hh
src/core/fragment/FrameIterator.hh
src/core/fragment/FrameIteratorWorker_.fwd.hh
src/core/fragment/FrameIteratorWorker_.hh
src/core/fragment/FrameList.cc
src/core/fragment/FrameList.fwd.hh
src/core/fragment/FrameList.hh
src/core/fragment/FrameListIterator_.hh
src/core/fragment/IndependentBBTorsionSRFD.ccA version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD)
src/core/fragment/IndependentBBTorsionSRFD.fwd.hhForward declaration for IndependentBBTorsionSRFD
src/core/fragment/IndependentBBTorsionSRFD.hhA version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD)
src/core/fragment/JumpingFrame.cc
src/core/fragment/JumpingFrame.fwd.hh
src/core/fragment/JumpingFrame.hh
src/core/fragment/JumpSRFD.cc
src/core/fragment/JumpSRFD.fwd.hh
src/core/fragment/JumpSRFD.hh
src/core/fragment/OrderedFragSet.cc
src/core/fragment/OrderedFragSet.fwd.hh
src/core/fragment/OrderedFragSet.hh
src/core/fragment/OrderedFragSetIterator_.hh
src/core/fragment/SecondaryStructure.ccSecondary structure will hold statistics about secondary structure predictions sources can be from
src/core/fragment/SecondaryStructure.fwd.hh
src/core/fragment/SecondaryStructure.hhSecondary structure will hold statistics about secondary structure predictions sources can be from
src/core/fragment/SecstructSRFD.cc
src/core/fragment/SecstructSRFD.hh
src/core/fragment/SingleResidueFragData.cc
src/core/fragment/SingleResidueFragData.fwd.hh
src/core/fragment/SingleResidueFragData.hh
src/core/fragment/SRFD_Implementations.hh
src/core/fragment/TorsionSRFD.hh
src/core/fragment/util.cc
src/core/fragment/util.hh
src/core/fragment/picking_old/FragmentLibraryManager.ccSingleton class for accessing fragment libraries
src/core/fragment/picking_old/FragmentLibraryManager.fwd.hhForward declaration for FragmentLibraryManager
src/core/fragment/picking_old/FragmentLibraryManager.hhSingleton class for accessing fragment libraries
src/core/fragment/picking_old/concepts/Book.fwd.hhForward declaration for core::fragment::picking_old::concepts
src/core/fragment/picking_old/concepts/Book.hhWrapper class demonstrating the Book concept
src/core/fragment/picking_old/concepts/Bookmark.fwd.hh
src/core/fragment/picking_old/concepts/Bookmark.hhStruct demonstrating Bookmark concept
src/core/fragment/picking_old/concepts/Extent.fwd.hhForward declaration for Extent
src/core/fragment/picking_old/concepts/Extent.hhClass demonstrating the Extent concept
src/core/fragment/picking_old/concepts/ExtentEvaluator.fwd.hh
src/core/fragment/picking_old/concepts/ExtentEvaluator.hh
src/core/fragment/picking_old/concepts/ExtentGenerator.fwd.hhForward declaration for core::fragment::picking_old::concepts::ExtentGenerator
src/core/fragment/picking_old/concepts/ExtentGenerator.hhClass demonstrating ExtentGenerator concept
src/core/fragment/picking_old/concepts/Librarian.fwd.hh
src/core/fragment/picking_old/concepts/Librarian.hhLibrarian template for sorting through and extracting desired fragments
src/core/fragment/picking_old/concepts/Library.fwd.hhForward declaration for core::fragment::concepts::Library
src/core/fragment/picking_old/concepts/Library.hhClass demonstrating the Library concept
src/core/fragment/picking_old/vall/util.ccUtility functions for interacting with VallLibrary
src/core/fragment/picking_old/vall/util.hhUtility functions for interacting with VallLibrary
src/core/fragment/picking_old/vall/vall_io.cc
src/core/fragment/picking_old/vall/vall_io.hhReading/writing of Vall libraries
src/core/fragment/picking_old/vall/VallLibrarian.ccLibrarian that picks fragments from the Vall
src/core/fragment/picking_old/vall/VallLibrarian.fwd.hhForward declaration for core::fragment::picking_old::vall::VallLibrarian
src/core/fragment/picking_old/vall/VallLibrarian.hhLibrarian that picks fragments from the Vall
src/core/fragment/picking_old/vall/VallLibrary.fwd.hhForward declaration for VallLibrary
src/core/fragment/picking_old/vall/VallLibrary.hhVall fragment library
src/core/fragment/picking_old/vall/VallResidue.ccClass for managing a line of the Vall fragment library
src/core/fragment/picking_old/vall/VallResidue.fwd.hhForward declaration for core::fragment::picking_old::vall:VallResidue
src/core/fragment/picking_old/vall/VallResidue.hhClass for managing a line of the Vall fragment library
src/core/fragment/picking_old/vall/VallSection.fwd.hhForward declaration for VallSection
src/core/fragment/picking_old/vall/VallSection.hhClass implementing the Book concept for a continuous section of lines in the Vall library
src/core/fragment/picking_old/vall/eval/ABEGOEval.ccScores a fragment based on abego identity
src/core/fragment/picking_old/vall/eval/ABEGOEval.fwd.hhForward declaration of core::fragment::picking_old::vall::eval::ABEGOEval
src/core/fragment/picking_old/vall/eval/ABEGOEval.hhScores a fragment based on ABEGO
src/core/fragment/picking_old/vall/eval/EnergyEval.ccScores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction
src/core/fragment/picking_old/vall/eval/EnergyEval.fwd.hhForward declaration of core::fragment::picking_old::vall::eval::EnergyEval
src/core/fragment/picking_old/vall/eval/EnergyEval.hhScores a fragment by inserting its backbone angles into a Pose and evaluating its energy using a given ScoreFunction
src/core/fragment/picking_old/vall/eval/IdentityEval.ccScores a fragment based on secondary structure identity and sequence identity
src/core/fragment/picking_old/vall/eval/IdentityEval.fwd.hhForward declaration of core::fragment::picking_old::vall::eval::IdentityEval
src/core/fragment/picking_old/vall/eval/IdentityEval.hhScores a fragment based on secondary structure identity and sequence identity
src/core/fragment/picking_old/vall/eval/VallFragmentEval.ccBase class for Vall ExtentEvaluator
src/core/fragment/picking_old/vall/eval/VallFragmentEval.fwd.hhForward declaration of core::fragment::picking_old::vall::eval::VallFragmentEval
src/core/fragment/picking_old/vall/eval/VallFragmentEval.hhBase class for Vall ExtentEvaluator
src/core/fragment/picking_old/vall/gen/LengthGen.ccDefault constant length fragment VallExtentGenerator
src/core/fragment/picking_old/vall/gen/LengthGen.fwd.hhForward declaration for core::fragment::picking_old::vall::gen::LengthGen
src/core/fragment/picking_old/vall/gen/LengthGen.hhDefault constant length fragment VallExtentGenerator
src/core/fragment/picking_old/vall/gen/SecStructGen.ccDefault constant length fragment VallExtentGenerator
src/core/fragment/picking_old/vall/gen/SecStructGen.fwd.hhForward declaration for core::fragment::picking_old::vall::gen::SecStructGen
src/core/fragment/picking_old/vall/gen/SecStructGen.hhGenerator that requires fragments to have a specific secondary structure string
src/core/fragment/picking_old/vall/gen/VallFragmentGen.ccBase class Vall ExtentGenerator
src/core/fragment/picking_old/vall/gen/VallFragmentGen.fwd.hhForward declaration for core::fragment::picking_old::vall::gen::VallFragmentGen
src/core/fragment/picking_old/vall/gen/VallFragmentGen.hhBase class Vall ExtentGenerator
src/core/fragment/picking_old/vall/scores/VallFragmentScore.fwd.hhForward declaration for core::fragment::picking_old::vall::scores::VallFragmentScore
src/core/fragment/picking_old/vall/scores/VallFragmentScore.hhBase Vall FragmentScore struct
src/core/graph/ArrayPool.fwd.hhForward declaration for ArrayPool classes
src/core/graph/ArrayPool.hhArrayPool class declaration and implementation
src/core/graph/DisjointSets.cc
src/core/graph/DisjointSets.fwd.hhDisjointSets class forward declaration
src/core/graph/DisjointSets.hh
src/core/graph/Graph.ccGraph base classes
src/core/graph/Graph.fwd.hhGraph base class forward declarations
src/core/graph/Graph.hhGeneric graph class header
src/core/graph/graph_util.cc
src/core/graph/graph_util.hhGeneric graph class header
src/core/graph/unordered_object_pool.fwd.hpp
src/core/graph/unordered_object_pool.hpp
src/core/graph/UpperEdgeGraph.cc
src/core/graph/UpperEdgeGraph.fwd.hh
src/core/graph/UpperEdgeGraph.hhTemplated graph for fast edge additions
src/core/grid/CartGrid.fwd.hh
src/core/grid/CartGrid.hh
src/core/id/AtomID.ccKinematics Atom identifier
src/core/id/AtomID.fwd.hhKinematics AtomID forward declarations header
src/core/id/AtomID.hh
src/core/id/AtomID_Map.fwd.hhCore::id::AtomID_Map forward declarations
src/core/id/AtomID_Map.hhMap from Atom identifiers to contained values class
src/core/id/AtomID_Mask.fwd.hhId::AtomID_Mask forward declarations header
src/core/id/AtomID_Mask.hhMap from Atom identifiers to booleans
src/core/id/CacheableAtomID_MapVector.fwd.hh
src/core/id/CacheableAtomID_MapVector.hh
src/core/id/DOF_ID.ccKinematics DOF identifier class
src/core/id/DOF_ID.fwd.hhKinematics DOF_ID forward declarations header
src/core/id/DOF_ID.hh
src/core/id/DOF_ID_Map.fwd.hhCore::id::DOF_ID_Map forward declarations
src/core/id/DOF_ID_Map.hhMap from Atom DOF identifiers to contained values class
src/core/id/DOF_ID_Mask.fwd.hhId::DOF_ID_Mask forward declarations header
src/core/id/DOF_ID_Mask.hhMap from Atom DOF identifiers to booleans
src/core/id/DOF_ID_Range.ccKinematics DOF identifier class
src/core/id/DOF_ID_Range.fwd.hhKinematics DOF_ID_Range forward declarations header
src/core/id/DOF_ID_Range.hh
src/core/id/Exceptions.cc
src/core/id/Exceptions.hh
src/core/id/JumpID.fwd.hhKinematics JumpID forward declarations header
src/core/id/JumpID.hh
src/core/id/NamedAtomID.ccKinematics Atom identifier
src/core/id/NamedAtomID.fwd.hh
src/core/id/NamedAtomID.hh
src/core/id/NamedStubID.cc
src/core/id/NamedStubID.fwd.hh
src/core/id/NamedStubID.hh
src/core/id/SequenceMapping.cc
src/core/id/SequenceMapping.fwd.hh
src/core/id/SequenceMapping.hh
src/core/id/TorsionID.ccKinematics Atom identifier
src/core/id/TorsionID.fwd.hhKinematics TorsionID forward declarations header
src/core/id/TorsionID.hh
src/core/id/TorsionID_Range.ccConformation torsion identifier class
src/core/id/TorsionID_Range.fwd.hhKinematics TorsionID_Range forward declarations header
src/core/id/TorsionID_Range.hh
src/core/id/types.hhCore::id package type declarations
src/core/import_pose/import_pose.ccVarious functions to construct Pose object(s) from PDB(s)
src/core/import_pose/import_pose.hhVarious functions to construct Pose object(s) from PDB(s)
src/core/import_pose/PDBSilentStruct.cc
src/core/import_pose/PDBSilentStruct.hh
src/core/import_pose/PDBSilentStructCreator.cc
src/core/import_pose/PDBSilentStructCreator.hh
src/core/import_pose/atom_tree_diffs/atom_tree_diff.cc
src/core/import_pose/atom_tree_diffs/atom_tree_diff.hh
src/core/import_pose/pose_stream/ExtendedPoseInputStream.cc
src/core/import_pose/pose_stream/ExtendedPoseInputStream.hh
src/core/import_pose/pose_stream/LazySilentFilePoseInputStream.cc
src/core/import_pose/pose_stream/LazySilentFilePoseInputStream.fwd.hh
src/core/import_pose/pose_stream/LazySilentFilePoseInputStream.hh
src/core/import_pose/pose_stream/MetaPoseInputStream.cc
src/core/import_pose/pose_stream/MetaPoseInputStream.hh
src/core/import_pose/pose_stream/PDBPoseInputStream.cc
src/core/import_pose/pose_stream/PDBPoseInputStream.fwd.hh
src/core/import_pose/pose_stream/PDBPoseInputStream.hh
src/core/import_pose/pose_stream/PoseInputStream.cc
src/core/import_pose/pose_stream/PoseInputStream.fwd.hh
src/core/import_pose/pose_stream/PoseInputStream.hh
src/core/import_pose/pose_stream/PoseOutputStream.hh
src/core/import_pose/pose_stream/SilentFilePoseInputStream.cc
src/core/import_pose/pose_stream/SilentFilePoseInputStream.fwd.hh
src/core/import_pose/pose_stream/SilentFilePoseInputStream.hh
src/core/import_pose/pose_stream/util.cc
src/core/import_pose/pose_stream/util.hh
src/core/io/ddg/PositionDdGInfo.cc
src/core/io/ddg/PositionDdGInfo.fwd.hh
src/core/io/ddg/PositionDdGInfo.hh
src/core/io/pdb/file_data.cc
src/core/io/pdb/file_data.fwd.hh
src/core/io/pdb/file_data.hh
src/core/io/pdb/pdb_dynamic_reader.cc
src/core/io/pdb/pdb_dynamic_reader.hhPDB Dynamic reader
src/core/io/pdb/pose_io.cc
src/core/io/pdb/pose_io.hh
src/core/io/raw_data/DecoyFileData.ccWrite decoys in "silent" format
src/core/io/raw_data/DecoyFileData.hh
src/core/io/raw_data/DecoyStruct.ccProtein-specific "silent" file reader and writer for mini
src/core/io/raw_data/DecoyStruct.hhSilent input file reader for mini
src/core/io/raw_data/DisulfideFile.cc
src/core/io/raw_data/DisulfideFile.hhA simple wrapper for a Disulfide File suitable for the -fix_disulf option
src/core/io/raw_data/Raw.fwd.hhForward declarations for raw data classes
src/core/io/raw_data/RawFileData.cc
src/core/io/raw_data/RawFileData.hhFileData base class
src/core/io/raw_data/RawStruct.ccStruct base class
src/core/io/raw_data/RawStruct.hhStruct base class
src/core/io/raw_data/ScoreFileData.ccWay to write out just the score using the SilentFile stuff
src/core/io/raw_data/ScoreFileData.hhWay to write out just the score using the SilentFile stuff
src/core/io/raw_data/ScoreStruct.ccWrite out only score information
src/core/io/raw_data/ScoreStruct.hhWrite out only the scores (equivalent to a scorefile)
src/core/io/sequence_comparation/DesignContrast.cc
src/core/io/sequence_comparation/DesignContrast.fwd.hh
src/core/io/sequence_comparation/DesignContrast.hh
src/core/io/serialization/serialize_pose.cc
src/core/io/serialization/serialize_pose.hh
src/core/io/silent/BasicSilentStructCreators.cc
src/core/io/silent/BasicSilentStructCreators.hh
src/core/io/silent/Binary_Util.cc
src/core/io/silent/Binary_Util.hh
src/core/io/silent/BinaryProteinSilentStruct.cc
src/core/io/silent/BinaryProteinSilentStruct.hh
src/core/io/silent/BinaryRNASilentStruct.cc
src/core/io/silent/BinaryRNASilentStruct.hh
src/core/io/silent/EnergyNames.fwd.hhSilent input file reader for mini
src/core/io/silent/EnergyNames.hhClass representing a set of energy names used in silent-file input/output
src/core/io/silent/ProteinSilentStruct.hhRepresentation of rosetta++ protein silent-file structures
src/core/io/silent/ProteinSilentStruct.tmpl.hhRepresentation of rosetta++ protein silent-file structures
src/core/io/silent/RNA_SilentStruct.ccRepresentation of rosetta++ protein silent-file structures
src/core/io/silent/RNA_SilentStruct.hhRepresentation of rosetta++ RNA silent-file structures
src/core/io/silent/ScoreFileSilentStruct.ccRepresentation of PDB files in a silent-file format
src/core/io/silent/ScoreFileSilentStruct.hhRepresentation of rosetta++ protein silent-file structures
src/core/io/silent/SharedSilentData.hhSilent input file reader for mini
src/core/io/silent/silent.fwd.hh
src/core/io/silent/SilentEnergy.hhSimple class for managing energies in SilentStruct objects
src/core/io/silent/SilentFileData.ccSilent input file reader for mini
src/core/io/silent/SilentFileData.fwd.hh
src/core/io/silent/SilentFileData.hhSilent input file reader for mini
src/core/io/silent/SilentStruct.ccSilent input file reader for mini
src/core/io/silent/SilentStruct.fwd.hh
src/core/io/silent/SilentStruct.hhSilent input file reader for mini
src/core/io/silent/SilentStructCreator.cc
src/core/io/silent/SilentStructCreator.fwd.hh
src/core/io/silent/SilentStructCreator.hhBase class for SilentStructCreators for the SilentStruct load-time factory registration scheme
src/core/io/silent/SilentStructFactory.ccFactory for creating various types of silent
src/core/io/silent/SilentStructFactory.fwd.hhSilent input file reader for mini
src/core/io/silent/SilentStructFactory.hhFactory for creating various types of SilentStruct objects
src/core/io/silent/util.ccUtility functions for silent-file classes
src/core/io/silent/util.hhUtility functions for silent-files
src/core/kinematics/all.fwd.hhCore::kinematics package forward declarations
src/core/kinematics/all.hhCore::kinematics package declarations
src/core/kinematics/AtomPointer.fwd.hhKinematics::AtomPointer2D forward declarations header
src/core/kinematics/AtomPointer.hhMap from Atom identifiers to Atom pointers
src/core/kinematics/AtomTree.ccAtom tree class
src/core/kinematics/AtomTree.fwd.hhKinematics::AtomTree forward declarations header
src/core/kinematics/AtomTree.hhAtom tree class
src/core/kinematics/AtomWithDOFChange.fwd.hhData structure for output-sensitie refold data class forward declaration
src/core/kinematics/AtomWithDOFChange.hhData structure for output-sensitie refold data class declaration
src/core/kinematics/constants.cc
src/core/kinematics/constants.hh
src/core/kinematics/DomainMap.fwd.hh
src/core/kinematics/DomainMap.hh
src/core/kinematics/Edge.ccFold tree edge class
src/core/kinematics/Edge.fwd.hhKinematics Edge forward declarations header
src/core/kinematics/Edge.hhFold tree edge class
src/core/kinematics/Exceptions.hhFold tree class
src/core/kinematics/FoldTree.ccFold tree class
src/core/kinematics/FoldTree.fwd.hhKinematics::FoldTree forward declarations header
src/core/kinematics/FoldTree.hhFold tree class
src/core/kinematics/Jump.ccKinematics Jump class
src/core/kinematics/Jump.fwd.hhKinematics Jump forward declarations header
src/core/kinematics/Jump.hhKinematics Jump class
src/core/kinematics/MinimizerMapBase.ccKinematics
src/core/kinematics/MinimizerMapBase.fwd.hhForward declaration of the minimizer-map base class for communicating between an AtomTree and the class that will use the AtomTree to perform some gradient-based minimization
src/core/kinematics/MinimizerMapBase.hhDeriviative classes from this base class will implement three virtual functions allowing the AtomTree to communicate with an outside Minimizer about how the degrees of freedom in the AtomTree should be minimized
src/core/kinematics/MoveMap.ccMove map
src/core/kinematics/MoveMap.fwd.hhKinematics MoveMap forward declarations header
src/core/kinematics/MoveMap.hhMove map
src/core/kinematics/ResidueCoordinateChangeList.cc
src/core/kinematics/ResidueCoordinateChangeList.fwd.hhAtomTree/Conformation communication vector class forward declaration
src/core/kinematics/ResidueCoordinateChangeList.hh
src/core/kinematics/RT.ccRotation + translation class
src/core/kinematics/RT.fwd.hhKinematics RT forward declarations header
src/core/kinematics/RT.hhRotation + translation class
src/core/kinematics/ShortestPathInFoldTree.ccHelper class to FoldTree: allows to measure distance in fold-trees
src/core/kinematics/ShortestPathInFoldTree.fwd.hhKinematics::ShortestPathInFoldTree forward declarations header
src/core/kinematics/ShortestPathInFoldTree.hhFold tree helper class
src/core/kinematics/Stub.ccStub class
src/core/kinematics/Stub.fwd.hhKinematics Stub forward declarations header
src/core/kinematics/Stub.hhStub class
src/core/kinematics/types.hhCore::kinematics package type declarations
src/core/kinematics/util.ccKinematics utility functions
src/core/kinematics/util.hhKinematics utility functions
src/core/kinematics/tree/Atom.fwd.hhKinematics Atom forward declarations header
src/core/kinematics/tree/Atom.hhKinematics Atom interface class
src/core/kinematics/tree/Atom_.ccKinematics Atom abstract base class
src/core/kinematics/tree/Atom_.hhKinematics Atom abstract base class
src/core/kinematics/tree/BondedAtom.ccKinematics
src/core/kinematics/tree/BondedAtom.hhKinematics
src/core/kinematics/tree/JumpAtom.ccJump atom
src/core/kinematics/tree/JumpAtom.hhJump atom
src/core/optimization/atom_tree_minimize.ccAtom tree minimization functions
src/core/optimization/atom_tree_minimize.hhAtom tree minimization functions
src/core/optimization/AtomNode.hh
src/core/optimization/AtomTreeMinimizer.ccHigh-level atom tree minimizer class
src/core/optimization/AtomTreeMinimizer.fwd.hhCore::optimization::AtomTreeMinimizer forward declarations
src/core/optimization/AtomTreeMinimizer.hhHigh-level atom tree minimizer class
src/core/optimization/AtomTreeMultifunc.cc
src/core/optimization/AtomTreeMultifunc.fwd.hhCore::optimization::AtomTreeMultifunc forward declarations
src/core/optimization/AtomTreeMultifunc.hhAtom tree multifunction class
src/core/optimization/cartesian_minimize.ccAtom tree minimization functions
src/core/optimization/cartesian_minimize.hh
src/core/optimization/CartesianMinimizer.ccHigh-level Cartesian minimizer class
src/core/optimization/CartesianMinimizer.fwd.hhCore::optimization::CartesianMinimizer forward declarations
src/core/optimization/CartesianMinimizer.hh
src/core/optimization/CartesianMinimizerMap.cc
src/core/optimization/CartesianMinimizerMap.fwd.hhForward declaration of CartesianMinimizerMap class
src/core/optimization/CartesianMinimizerMap.hhClass for connecting DOFs in the atom tree to DOFs optimized by the AtomTreeMinimizer
src/core/optimization/CartesianMultifunc.cc
src/core/optimization/CartesianMultifunc.fwd.hh
src/core/optimization/CartesianMultifunc.hh
src/core/optimization/DOF_Node.fwd.hh
src/core/optimization/DOF_Node.hh
src/core/optimization/GA_Minimizer.ccMinimizer based on Genetic Algorithm
src/core/optimization/GA_Minimizer.hhMinimizer based on Genetic Algorithm
src/core/optimization/LineMinimizer.ccLine minimizer classes
src/core/optimization/LineMinimizer.fwd.hhCore::optimization::LineMinimizer forward declarations
src/core/optimization/LineMinimizer.hhLine minimizer classes
src/core/optimization/Minimizer.ccMinimizer class
src/core/optimization/Minimizer.fwd.hhCore::optimization::Minimizer forward declarations
src/core/optimization/Minimizer.hhSimple low-level minimizer class
src/core/optimization/MinimizerMap.cc
src/core/optimization/MinimizerMap.fwd.hhForward declaration of MinimizerMap class
src/core/optimization/MinimizerMap.hhClass for connecting DOFs in the atom tree to DOFs optimized by the AtomTreeMinimizer
src/core/optimization/MinimizerOptions.ccMinimizer options class implementation
src/core/optimization/MinimizerOptions.fwd.hhCore::optimization::MinimizerOptions forward declarations
src/core/optimization/MinimizerOptions.hhMinimizer options class
src/core/optimization/Multifunc.fwd.hhCore::optimization::Multifunc forward declarations
src/core/optimization/Multifunc.hhMultifunction interface class
src/core/optimization/NumericalDerivCheckResult.cc
src/core/optimization/NumericalDerivCheckResult.fwd.hhForward declaration for nuerical derivative check results classes
src/core/optimization/NumericalDerivCheckResult.hhDeclaration for nuerical derivative check results classes
src/core/optimization/ParticleSwarmMinimizer.cc
src/core/optimization/ParticleSwarmMinimizer.fwd.hh
src/core/optimization/ParticleSwarmMinimizer.hh
src/core/optimization/SingleResidueMultifunc.cc
src/core/optimization/SingleResidueMultifunc.fwd.hh
src/core/optimization/SingleResidueMultifunc.hh
src/core/optimization/types.hhCore::optimization optimization type declarations
src/core/optimization/symmetry/sym_atom_tree_minimize.cc
src/core/optimization/symmetry/sym_atom_tree_minimize.hh
src/core/optimization/symmetry/SymAtomTreeMinimizer.ccHigh-level atom tree minimizer class for symmetrical minimization
src/core/optimization/symmetry/SymAtomTreeMinimizer.fwd.hh
src/core/optimization/symmetry/SymAtomTreeMinimizer.hh
src/core/optimization/symmetry/SymAtomTreeMultifunc.cc
src/core/optimization/symmetry/SymAtomTreeMultifunc.hh
src/core/optimization/symmetry/SymMinimizerMap.cc
src/core/optimization/symmetry/SymMinimizerMap.fwd.hh
src/core/optimization/symmetry/SymMinimizerMap.hh
src/core/pack/all.fwd.hhCore::pack package forward declarations
src/core/pack/all.hhCore::pack package declarations
src/core/pack/make_symmetric_task.cc
src/core/pack/make_symmetric_task.hhUtility functions for handling with symmetric conformations
src/core/pack/min_pack.ccPack rotamers with minimization module
src/core/pack/min_pack.hhPack and minimize sidechains
src/core/pack/optimizeH.ccStandard hydrogen optimization subroutine
src/core/pack/optimizeH.hhDeclaration of standard hydrogen optimization subroutine
src/core/pack/pack_missing_sidechains.ccFunction to fix missing sidechains in input PDBs (especially those surface lysines that get sidechain-backbone clashes!)
src/core/pack/pack_missing_sidechains.hhHeader for subroutine to run rotamer trials on residues missing sidechain density in a PDB
src/core/pack/pack_rotamers.ccPack rotamers module
src/core/pack/pack_rotamers.hhPack rotamers module header
src/core/pack/packer_neighbors.ccCreates a graph that describes the possible connectivity induced by designing-in larger side chains
src/core/pack/packer_neighbors.hhCreates a graph that describes the possible connectivity induced by designing-in larger side chains
src/core/pack/rotamer_trials.ccRotamer trials module
src/core/pack/rotamer_trials.hhRotamer trials module header
src/core/pack/rtmin.ccRotamer trials with minimization module header. Originally concieved of and implemented in Rosetta++ by Chu Wang
src/core/pack/rtmin.hhRotamer trials with minimization module header
src/core/pack/annealer/AnnealerFactory.ccAnnealer Factory class implementation
src/core/pack/annealer/AnnealerFactory.fwd.hhAnnealer Factory class forward declaration
src/core/pack/annealer/AnnealerFactory.hh
src/core/pack/annealer/DebuggingAnnealer.ccDebugging annealer class implementation
src/core/pack/annealer/DebuggingAnnealer.fwd.hhDebugging annealer class forward declaration
src/core/pack/annealer/DebuggingAnnealer.hhDebugging annealer class declaration
src/core/pack/annealer/FASTERAnnealer.cc
src/core/pack/annealer/FASTERAnnealer.fwd.hh
src/core/pack/annealer/FASTERAnnealer.hh
src/core/pack/annealer/FixbbCoupledRotamerSimAnnealer.ccPacker's standard simulated annealing class implementation
src/core/pack/annealer/FixbbCoupledRotamerSimAnnealer.fwd.hh
src/core/pack/annealer/FixbbCoupledRotamerSimAnnealer.hhPacker's standard annealer class declaration
src/core/pack/annealer/FixbbLinkingRotamerSimAnnealer.ccPacker's standard simulated annealing class implementation
src/core/pack/annealer/FixbbLinkingRotamerSimAnnealer.fwd.hh
src/core/pack/annealer/FixbbLinkingRotamerSimAnnealer.hhPacker's standard annealer class declaration
src/core/pack/annealer/FixbbSimAnnealer.ccPacker's standard simulated annealing class implementation
src/core/pack/annealer/FixbbSimAnnealer.fwd.hhPacker's standard annealer class forward declaration
src/core/pack/annealer/FixbbSimAnnealer.hhPacker's standard annealer class declaration, originally written by Brian Kuhlman and factored into base and derived classes by Jenny Hu
src/core/pack/annealer/MultiCoolAnnealer.ccMultiple low-temperature cooling cycles annealer class definition
src/core/pack/annealer/MultiCoolAnnealer.fwd.hhMultiple low-temperature cooling cycles annealer class forward declaration
src/core/pack/annealer/MultiCoolAnnealer.hhMultiple low-temperature cooling cycles annealer class declaration
src/core/pack/annealer/RotamerAssigningAnnealer.ccAnnealer class that assigns rotamers implementation
src/core/pack/annealer/RotamerAssigningAnnealer.fwd.hhResidue assigning annealer class forward declaration
src/core/pack/annealer/RotamerAssigningAnnealer.hhResidue assigning annealer class declaration
src/core/pack/annealer/SimAnnealerBase.ccPacker's simulated annealing base class implementation
src/core/pack/annealer/SimAnnealerBase.fwd.hhPacker's annealer base class forward declaration
src/core/pack/annealer/SimAnnealerBase.hhPacker's simulated annealing base class implementation
src/core/pack/dunbrack/ChiSet.cc
src/core/pack/dunbrack/ChiSet.fwd.hh
src/core/pack/dunbrack/ChiSet.hh
src/core/pack/dunbrack/CoarseRotamer.cc
src/core/pack/dunbrack/CoarseRotamer.fwd.hh
src/core/pack/dunbrack/CoarseRotamer.hh
src/core/pack/dunbrack/CoarseSingleResidueLibrary.cc
src/core/pack/dunbrack/CoarseSingleResidueLibrary.fwd.hh
src/core/pack/dunbrack/CoarseSingleResidueLibrary.hh
src/core/pack/dunbrack/DunbrackConstraint.cc
src/core/pack/dunbrack/DunbrackConstraint.fwd.hh
src/core/pack/dunbrack/DunbrackConstraint.hh
src/core/pack/dunbrack/DunbrackConstraintCreator.hhBase class for ConstraintCreators for the Constraint load-time factory registration scheme
src/core/pack/dunbrack/DunbrackEnergy.ccDunbrack energy method implementation
src/core/pack/dunbrack/DunbrackEnergy.fwd.hh
src/core/pack/dunbrack/DunbrackEnergy.hh
src/core/pack/dunbrack/DunbrackEnergyCreator.hh
src/core/pack/dunbrack/DunbrackRotamer.cc
src/core/pack/dunbrack/DunbrackRotamer.fwd.hh
src/core/pack/dunbrack/DunbrackRotamer.hh
src/core/pack/dunbrack/RotamerConstraint.cc
src/core/pack/dunbrack/RotamerConstraint.fwd.hh
src/core/pack/dunbrack/RotamerConstraint.hh
src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.fwd.hh
src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.hh
src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh
src/core/pack/dunbrack/RotamerLibrary.cc
src/core/pack/dunbrack/RotamerLibrary.fwd.hhScore function class
src/core/pack/dunbrack/RotamerLibrary.hh
src/core/pack/dunbrack/RotamerLibraryScratchSpace.cc
src/core/pack/dunbrack/RotamerLibraryScratchSpace.fwd.hh
src/core/pack/dunbrack/RotamerLibraryScratchSpace.hh
src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.cc
src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.fwd.hh
src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.hh
src/core/pack/dunbrack/SemiRotamericSingleResidueDunbrackLibrary.tmpl.hh
src/core/pack/dunbrack/SingleLigandRotamerLibrary.cc
src/core/pack/dunbrack/SingleLigandRotamerLibrary.hh
src/core/pack/dunbrack/SingleResidueDunbrackLibrary.cc
src/core/pack/dunbrack/SingleResidueDunbrackLibrary.fwd.hh
src/core/pack/dunbrack/SingleResidueDunbrackLibrary.hh
src/core/pack/dunbrack/SingleResidueDunbrackLibrary.tmpl.hh
src/core/pack/interaction_graph/AdditionalBackgroundNodesInteractionGraph.hhInteraction graph which can handle some residues not changing during packing
src/core/pack/interaction_graph/AminoAcidNeighborSparseMatrix.fwd.hhSparse Matrix class for rotamer pair energy storage forward declaration
src/core/pack/interaction_graph/AminoAcidNeighborSparseMatrix.hhAmino acid neighbor sparse matrix template class
src/core/pack/interaction_graph/DensePDInteractionGraph.ccDense Edge-Matrix, Pairwise Decomposable interaction graph class implementation
src/core/pack/interaction_graph/DensePDInteractionGraph.fwd.hh
src/core/pack/interaction_graph/DensePDInteractionGraph.hhDense Edge-Matrix, Pairwise Decomposable interaction graph class header This graph does not take advantage of the memory-saving AANeighborSparseMatrix for the storage of RPEs (rotamer pair energies); for this reason it's a little bit faster and weights a little less than the PDInteractionGraph for fixed-sequence repackings -- memory becomes a significant issue for design simulations, and this graph should not be used for that purpose
src/core/pack/interaction_graph/DoubleDensePDInteractionGraph.cc
src/core/pack/interaction_graph/DoubleDensePDInteractionGraph.fwd.hh
src/core/pack/interaction_graph/DoubleDensePDInteractionGraph.hhDouble-The-Memory interaction graph which stores interaction energies for a rotamer and all of its neighbors in a single row in memory
src/core/pack/interaction_graph/DoubleLazyInteractionGraph.ccInteraction graph that computes each rotamer pair energy at most once
src/core/pack/interaction_graph/DoubleLazyInteractionGraph.fwd.hhInteraction graph that computes each rotamer pair energy at most once
src/core/pack/interaction_graph/DoubleLazyInteractionGraph.hhInteraction graph that computes each rotamer pair energy at most once
src/core/pack/interaction_graph/FASTERInteractionGraph.cc
src/core/pack/interaction_graph/FASTERInteractionGraph.fwd.hh
src/core/pack/interaction_graph/FASTERInteractionGraph.hh
src/core/pack/interaction_graph/FixedBBInteractionGraph.ccPrecomputed interaction graph class
src/core/pack/interaction_graph/FixedBBInteractionGraph.fwd.hhInteraction graph base class for fixed-backbone packing
src/core/pack/interaction_graph/FixedBBInteractionGraph.hhInteraction graph base class for fixed-backbone packing
src/core/pack/interaction_graph/HPatchEnergy.cc
src/core/pack/interaction_graph/HPatchEnergy.fwd.hh
src/core/pack/interaction_graph/HPatchEnergy.hh
src/core/pack/interaction_graph/HPatchEnergyCreator.hh
src/core/pack/interaction_graph/HPatchInteractionGraph.fwd.hhForward header for an IG that designs against hydrophobic area on the surface of proteins
src/core/pack/interaction_graph/HPatchInteractionGraph.hhInteraction graph which implements a non-PD score that optimizes against surface hydrophobic patches
src/core/pack/interaction_graph/InteractionGraphBase.ccInteraction graph base class
src/core/pack/interaction_graph/InteractionGraphBase.fwd.hhInteractionGraph base class forward declaration
src/core/pack/interaction_graph/InteractionGraphBase.hhInteraction graph base class header
src/core/pack/interaction_graph/InteractionGraphFactory.ccInteration graph factory class definition
src/core/pack/interaction_graph/InteractionGraphFactory.fwd.hhInteration graph factory class forward declaration
src/core/pack/interaction_graph/InteractionGraphFactory.hhInteration graph factory class declaration
src/core/pack/interaction_graph/LazyInteractionGraph.ccInteraction graph that computes each rotamer pair energy at most once
src/core/pack/interaction_graph/LazyInteractionGraph.fwd.hhInteraction graph that computes each rotamer pair energy at most once
src/core/pack/interaction_graph/LazyInteractionGraph.hhInteraction graph that computes each rotamer pair energy at most once
src/core/pack/interaction_graph/LinearMemoryInteractionGraph.cc
src/core/pack/interaction_graph/LinearMemoryInteractionGraph.fwd.hh
src/core/pack/interaction_graph/LinearMemoryInteractionGraph.hh
src/core/pack/interaction_graph/OnTheFlyInteractionGraph.cc
src/core/pack/interaction_graph/OnTheFlyInteractionGraph.fwd.hh
src/core/pack/interaction_graph/OnTheFlyInteractionGraph.hh
src/core/pack/interaction_graph/PDInteractionGraph.ccPairwise Decomposable interaction graph class
src/core/pack/interaction_graph/PDInteractionGraph.fwd.hhSparse pairwise decomposable interaction graph forward declaration
src/core/pack/interaction_graph/PDInteractionGraph.hhPairwise Decomposable interaction graph class header
src/core/pack/interaction_graph/PrecomputedPairEnergiesInteractionGraph.ccPrecomputed interaction graph class
src/core/pack/interaction_graph/PrecomputedPairEnergiesInteractionGraph.fwd.hhPrecomputed Pair Energies Interaction Graph forward declaration
src/core/pack/interaction_graph/PrecomputedPairEnergiesInteractionGraph.hhPrecomputed interaction graph class header
src/core/pack/interaction_graph/RotamerDots.ccRotamerDots classes files - ported from rosetta++
src/core/pack/interaction_graph/RotamerDots.fwd.hhRotamerDots classes, forward declaration - ported from rosetta++
src/core/pack/interaction_graph/RotamerDots.hhRotamerDots classes header files - ported from rosetta++
src/core/pack/interaction_graph/SimpleInteractionGraph.cc
src/core/pack/interaction_graph/SimpleInteractionGraph.fwd.hh
src/core/pack/interaction_graph/SimpleInteractionGraph.hh
src/core/pack/interaction_graph/SparseMatrixIndex.fwd.hhHelper class for AminoAcidNeighborSparseMatrix forward declaration
src/core/pack/interaction_graph/SparseMatrixIndex.hh
src/core/pack/interaction_graph/SurfaceEnergy.cc
src/core/pack/interaction_graph/SurfaceEnergy.fwd.hh
src/core/pack/interaction_graph/SurfaceEnergy.hh
src/core/pack/interaction_graph/SurfaceEnergyCreator.hh
src/core/pack/interaction_graph/SurfaceInteractionGraph.fwd.hhForward header for an IG that designs against hydrophobic area on the surface of proteins
src/core/pack/interaction_graph/SurfaceInteractionGraph.hhInteraction graph which implements a non-PD, environment-dependent score for surface residues
src/core/pack/interaction_graph/SurfacePotential.cc
src/core/pack/interaction_graph/SurfacePotential.hh
src/core/pack/rotamer_set/bb_independent_rotamers.ccBuild rotamers for residue type given neutral beckbone
src/core/pack/rotamer_set/bb_independent_rotamers.hhBunch of utility functions used in enzdes
src/core/pack/rotamer_set/BumpSelector.ccBump selector class implementation
src/core/pack/rotamer_set/BumpSelector.hh
src/core/pack/rotamer_set/ContinuousRotamerSet.cc
src/core/pack/rotamer_set/ContinuousRotamerSet.fwd.hh
src/core/pack/rotamer_set/ContinuousRotamerSet.hh
src/core/pack/rotamer_set/FixbbRotamerSets.ccFixed-backbone Residue Sets interface class implementation
src/core/pack/rotamer_set/FixbbRotamerSets.fwd.hhFixed-backbone Residue Sets interface class foward declarations
src/core/pack/rotamer_set/FixbbRotamerSets.hh
src/core/pack/rotamer_set/rotamer_building_functions.cc
src/core/pack/rotamer_set/rotamer_building_functions.hh
src/core/pack/rotamer_set/RotamerCouplings.fwd.hh
src/core/pack/rotamer_set/RotamerCouplings.hh
src/core/pack/rotamer_set/RotamerLinks.fwd.hh
src/core/pack/rotamer_set/RotamerLinks.hh
src/core/pack/rotamer_set/RotamerSet.cc
src/core/pack/rotamer_set/RotamerSet.fwd.hhResidue set class forward declarations
src/core/pack/rotamer_set/RotamerSet.hh
src/core/pack/rotamer_set/RotamerSet_.ccAmino acid rotamer set class implementation
src/core/pack/rotamer_set/RotamerSet_.fwd.hhRotamer set implementation class forward declarations
src/core/pack/rotamer_set/RotamerSet_.hhRotamer set implementation class
src/core/pack/rotamer_set/RotamerSetFactory.cc
src/core/pack/rotamer_set/RotamerSetFactory.fwd.hhResidue Set Facotry class forward declaration
src/core/pack/rotamer_set/RotamerSetFactory.hhResidue Set Factory class
src/core/pack/rotamer_set/RotamerSetOperation.ccRotamer set operation implementation
src/core/pack/rotamer_set/RotamerSetOperation.fwd.hhRotamer set operation forward declaration
src/core/pack/rotamer_set/RotamerSetOperation.hhRotamer set operation class
src/core/pack/rotamer_set/RotamerSets.cc
src/core/pack/rotamer_set/RotamerSets.fwd.hhResidue Sets class foward declarations
src/core/pack/rotamer_set/RotamerSets.hh
src/core/pack/rotamer_set/RotamerSetsBase.cc
src/core/pack/rotamer_set/RotamerSetsBase.fwd.hh
src/core/pack/rotamer_set/RotamerSetsBase.hh
src/core/pack/rotamer_set/RotamerSubset.cc
src/core/pack/rotamer_set/RotamerSubset.fwd.hh
src/core/pack/rotamer_set/RotamerSubset.hh
src/core/pack/rotamer_set/RotamerSubsets.cc
src/core/pack/rotamer_set/RotamerSubsets.fwd.hhResidue Subsets class foward declarations
src/core/pack/rotamer_set/RotamerSubsets.hh
src/core/pack/rotamer_set/UnboundRotamersOperation.cc
src/core/pack/rotamer_set/UnboundRotamersOperation.fwd.hh
src/core/pack/rotamer_set/UnboundRotamersOperation.hh
src/core/pack/rotamer_set/WaterAnchorInfo.cc
src/core/pack/rotamer_set/WaterAnchorInfo.fwd.hh
src/core/pack/rotamer_set/WaterAnchorInfo.hh
src/core/pack/rotamer_set/WaterPackingInfo.cc
src/core/pack/rotamer_set/WaterPackingInfo.fwd.hh
src/core/pack/rotamer_set/WaterPackingInfo.hh
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSet_.ccAmino acid rotamer set class implementation for symmetric packing
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSet_.fwd.hh
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSet_.hhRotamer set implementation class for symmetric packing
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSetFactory.cc
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSetFactory.fwd.hh
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSetFactory.hhResidue Set Factory class for symmetric packing
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSets.cc
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSets.fwd.hh
src/core/pack/rotamer_set/symmetry/SymmetricRotamerSets.hh
src/core/pack/scmin/AtomTreeCollection.ccImplementation for the classes holding sets of AtomTrees used during variuos packing+minimizing schemes
src/core/pack/scmin/AtomTreeCollection.fwd.hh
src/core/pack/scmin/AtomTreeCollection.hhForward declaration for the classes holding sets of AtomTrees used during variuos packing+minimizing schemes
src/core/pack/scmin/SCMinMinimizerMap.ccClass for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer
src/core/pack/scmin/SCMinMinimizerMap.fwd.hhFoward declaration for the class identifying sidechain DOFs in the AtomTree which are free during any particular call to the minimizer
src/core/pack/scmin/SCMinMinimizerMap.hhClass for identifying the sidechain DOFs in the AtomTree which are free during any particular call to the minimizer
src/core/pack/scmin/SCMinMultifunc.ccClass for interfacing with the minimizer during sidechain minimization
src/core/pack/scmin/SCMinMultifunc.fwd.hhForward declaration of the interface class to the minimizer during sidechain minimization
src/core/pack/scmin/SCMinMultifunc.hhClass for interfacing with the minimizer during sidechain minimization
src/core/pack/scmin/SidechainStateAssignment.cc
src/core/pack/scmin/SidechainStateAssignment.hhDeclaration for the class that holds a state assignment for an entire system under continuous sidechain optimization
src/core/pack/task/IGEdgeReweightContainer.cc
src/core/pack/task/IGEdgeReweightContainer.fwd.hh
src/core/pack/task/IGEdgeReweightContainer.hh
src/core/pack/task/PackerTask.ccTask class to describe packer's behavior
src/core/pack/task/PackerTask.fwd.hhTask class to describe packer's behavior forward declaration
src/core/pack/task/PackerTask.hhTask class to describe packer's behavior header
src/core/pack/task/PackerTask_.cc
src/core/pack/task/PackerTask_.fwd.hhImplementation class for task class to describe packer's behavior forward declaration Almost all of rosetta needs to use packer tasks, but very little of rosetta needs to see how it behaves internally
src/core/pack/task/PackerTask_.hhImplementation class for task class to describe packer's behavior header Almost all of rosetta needs to use packer tasks, but very little of rosetta needs to see how it behaves internally
src/core/pack/task/ResfileReader.ccImplementation of resfile reader and its command classes
src/core/pack/task/ResfileReader.fwd.hh
src/core/pack/task/ResfileReader.hhHeader of classes for resfile options
src/core/pack/task/RotamerSampleOptions.cc
src/core/pack/task/RotamerSampleOptions.hhClass to describe rotamer construction header
src/core/pack/task/TaskFactory.cc
src/core/pack/task/TaskFactory.fwd.hh
src/core/pack/task/TaskFactory.hhTask class to describe packer's behavior header
src/core/pack/task/operation/NoRepackDisulfides.ccPrevent disulfides from being repacked; assumes disulfide info in Pose is up-to-date
src/core/pack/task/operation/NoRepackDisulfides.fwd.hhForward declaration for NoRepackDisulfides
src/core/pack/task/operation/NoRepackDisulfides.hhPrevent disulfides from being repacked; assumes disulfide info in Pose is up-to-date
src/core/pack/task/operation/NoRepackDisulfidesCreator.hh
src/core/pack/task/operation/OperateOnCertainResidues.ccClass to support the general case of configuring PackerTask at the ResidueLevelTask level in some way, with an optional filter to limit the effects to certain residues
src/core/pack/task/operation/OperateOnCertainResidues.fwd.hhForward declaration of a class that performs an operation on a packer task, in a configurable residue-specific manner
src/core/pack/task/operation/OperateOnCertainResidues.hhClass to support the general case of configuring PackerTask at the ResidueLevelTask level in some way, with an optional filter to limit the effects to certain residues
src/core/pack/task/operation/OperateOnCertainResiduesCreator.hh
src/core/pack/task/operation/OptCysHG.ccRun optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides()
src/core/pack/task/operation/OptCysHG.fwd.hhForward declaration for OptCysHG
src/core/pack/task/operation/OptCysHG.hhRun optH on non-disulfided bonded CYS only; meant to relieve any clashes caused by swapping of CYD->CYS after calling Conformation::detect_disulfides()
src/core/pack/task/operation/OptCysHGCreator.hh
src/core/pack/task/operation/OptH.ccRun optH
src/core/pack/task/operation/OptH.fwd.hhForward declaration for OptH
src/core/pack/task/operation/OptH.hhRun optH
src/core/pack/task/operation/OptHCreator.hh
src/core/pack/task/operation/ReplicateTask.cc
src/core/pack/task/operation/ReplicateTask.fwd.hhForward declaration for ReplicateTask
src/core/pack/task/operation/ReplicateTask.hh
src/core/pack/task/operation/ReplicateTaskCreator.hh
src/core/pack/task/operation/ResFilter.fwd.hhForward declaration of a class that takes a pose and a residue index, and returns true or false
src/core/pack/task/operation/ResFilter.hhAbstract base class that takes a pose and a residue index, and returns true or false
src/core/pack/task/operation/ResFilterCreator.fwd.hh
src/core/pack/task/operation/ResFilterCreator.hh
src/core/pack/task/operation/ResFilterCreators.hhDeclaration for the class that connects ResFilters with the ResFilterFactory
src/core/pack/task/operation/ResFilterFactory.cc
src/core/pack/task/operation/ResFilterFactory.fwd.hh
src/core/pack/task/operation/ResFilterFactory.hh
src/core/pack/task/operation/ResFilterRegistrator.hh
src/core/pack/task/operation/ResFilters.cc
src/core/pack/task/operation/ResFilters.fwd.hhCore-level (very general) classes that take a pose and a residue index, and returns true or false
src/core/pack/task/operation/ResFilters.hhCore-level (very general) classes that take a pose and a residue index, and return true or false
src/core/pack/task/operation/ResLvlTaskOperation.fwd.hhForward declaration of a class that performs an operation on ResidueLevelTask usually by a TaskFactory right after the task's construction
src/core/pack/task/operation/ResLvlTaskOperation.hhClass that performs an operation on ResidueLevelTask, usually by a PackerTaskFactory right after the task's construction
src/core/pack/task/operation/ResLvlTaskOperationCreator.fwd.hh
src/core/pack/task/operation/ResLvlTaskOperationCreator.hh
src/core/pack/task/operation/ResLvlTaskOperationCreators.hhDeclaration for the class that connects ResLvlTaskOperations with the ResLvlTaskOperationFactory
src/core/pack/task/operation/ResLvlTaskOperationFactory.cc
src/core/pack/task/operation/ResLvlTaskOperationFactory.fwd.hh
src/core/pack/task/operation/ResLvlTaskOperationFactory.hh
src/core/pack/task/operation/ResLvlTaskOperationRegistrator.hh
src/core/pack/task/operation/ResLvlTaskOperations.cc
src/core/pack/task/operation/ResLvlTaskOperations.fwd.hhForward declaration for core-level (very general) derived classes that wrap widely-used methods of the ResidueLevelTask interface. These are used by higher-level TaskOperations that allow the user to configure the behavior of PackerTasks that are created by TaskFactory
src/core/pack/task/operation/ResLvlTaskOperations.hhCore-level (very general) derived classes that wrap widely-used methods of the ResidueLevelTask interface. These are used by higher-level TaskOperations that allow the user to configure the behavior of PackerTasks that are created by TaskFactory
src/core/pack/task/operation/RestrictToInterface.cc
src/core/pack/task/operation/RestrictToInterface.hh
src/core/pack/task/operation/TaskOperation.ccAn operation to perform on a packer task -- usually, by a PackerTaskFactory right after the task's construction
src/core/pack/task/operation/TaskOperation.fwd.hhForward declaration of a class that performs an operation on a packer task, usually, by a PackerTaskFactory right after the task's construction
src/core/pack/task/operation/TaskOperation.hhAn operation to perform on a packer task -- usually, by a PackerTaskFactory right after the task's construction
src/core/pack/task/operation/TaskOperationCreator.fwd.hh
src/core/pack/task/operation/TaskOperationCreator.hh
src/core/pack/task/operation/TaskOperationCreators.hhDeclaration for the class that connects TaskOperations with the TaskOperationFactory
src/core/pack/task/operation/TaskOperationFactory.cc
src/core/pack/task/operation/TaskOperationFactory.fwd.hh
src/core/pack/task/operation/TaskOperationFactory.hh
src/core/pack/task/operation/TaskOperationRegistrator.hh
src/core/pack/task/operation/TaskOperations.cc
src/core/pack/task/operation/TaskOperations.fwd.hh
src/core/pack/task/operation/TaskOperations.hhAn operation to perform on a packer task -- usually, by a PackerTaskFactory right after the task's construction This is an incomplete list. Freely define your own TaskOperation and hand it to a PackerTaskFactory
src/core/pack/task/operation/util/interface_vector_calculate.cc
src/core/pack/task/operation/util/interface_vector_calculate.hhCalculates an interface definition based on a short distance
src/core/pose/annotated_sequence.ccUtility functions for making poses from sequences
src/core/pose/annotated_sequence.hh
src/core/pose/MiniPose.ccMiniPose class
src/core/pose/MiniPose.fwd.hhMiniPose forward declarations header
src/core/pose/MiniPose.hhMiniPose class
src/core/pose/PDBInfo.ccClass to hold PDB information so it's not loose in the pose
src/core/pose/PDBInfo.fwd.hhFwd declaration of classes defined in pose/PDBInfo
src/core/pose/PDBInfo.hhPose information so it's not loose in the pose
src/core/pose/PDBPoseMap.ccClass to allow querying for pose resid with pdb chain/seqpos
src/core/pose/PDBPoseMap.fwd.hhFwd declaration of classes defined in pose/PDBPoseMap
src/core/pose/PDBPoseMap.hhClass to allow querying for pose resid with pdb chain/seqpos
src/core/pose/Pose.ccPose class
src/core/pose/Pose.fwd.hhPose forward declarations header
src/core/pose/Pose.hhPose class
src/core/pose/Remarks.fwd.hh
src/core/pose/Remarks.hh
src/core/pose/util.ccPose class utilities
src/core/pose/util.hhPose utilities
src/core/pose/util.tmpl.hh
src/core/pose/datacache/cacheable_observers.cc
src/core/pose/datacache/cacheable_observers.fwd.hhForward declarations for a bunch of CacheableObserver implementations
src/core/pose/datacache/cacheable_observers.hhFile that has class definitions for a bunch of general CacheableObserver implementations
src/core/pose/datacache/CacheableDataType.hhEnum indexing the data types stored in a Pose's internal DataCache
src/core/pose/datacache/CacheableObserver.ccBase class for Pose/Conformation observers that are stored in a Pose's DataCache
src/core/pose/datacache/CacheableObserver.fwd.hhForward declaration for CacheableObserver
src/core/pose/datacache/CacheableObserver.hhBase class for Pose/Conformation observers that are stored in a Pose's ObserverCache
src/core/pose/datacache/CacheableObserverType.hhEnum indexing the observer types stored in a Pose's internal ObserverCache
src/core/pose/datacache/CacheablePoseRawPtr.fwd.hh
src/core/pose/datacache/CacheablePoseRawPtr.hh
src/core/pose/datacache/ObserverCache.ccA DataCache storing objects derived from core::pose::datacache::CacheableData
src/core/pose/datacache/ObserverCache.fwd.hhForward declaration for ObserverCache
src/core/pose/datacache/ObserverCache.hh
src/core/pose/datacache/PositionConservedResiduesStore.cc
src/core/pose/datacache/PositionConservedResiduesStore.fwd.hh
src/core/pose/datacache/PositionConservedResiduesStore.hh
src/core/pose/metrics/CalculatorFactory.ccCalculatorFactory class
src/core/pose/metrics/CalculatorFactory.hh
src/core/pose/metrics/PoseMetricCalculatorBase.fwd.hh
src/core/pose/metrics/PoseMetricCalculatorBase.hh
src/core/pose/metrics/PoseMetricContainer.ccPoseMetricContainer class
src/core/pose/metrics/PoseMetricContainer.fwd.hh
src/core/pose/metrics/PoseMetricContainer.hhContainer for managing PoseMetricCalculators
src/core/pose/metrics/simple_calculators/InterfaceDefinitionCalculatorBase.cc
src/core/pose/metrics/simple_calculators/InterfaceDefinitionCalculatorBase.hh
src/core/pose/metrics/simple_calculators/InterfaceDeltaEnergeticsCalculator.cc
src/core/pose/metrics/simple_calculators/InterfaceDeltaEnergeticsCalculator.hh
src/core/pose/metrics/simple_calculators/InterfaceNeighborDefinitionCalculator.cc
src/core/pose/metrics/simple_calculators/InterfaceNeighborDefinitionCalculator.hh
src/core/pose/metrics/simple_calculators/InterfaceSasaDefinitionCalculator.ccSasaCalculator class
src/core/pose/metrics/simple_calculators/InterfaceSasaDefinitionCalculator.hh
src/core/pose/metrics/simple_calculators/SasaCalculator.cc
src/core/pose/metrics/simple_calculators/SasaCalculator.hh
src/core/pose/signals/ConformationEvent.fwd.hhForward declaration for core::pose::signals::ConformationEvent
src/core/pose/signals/ConformationEvent.hhSignal for a conformation change in a Pose
src/core/pose/signals/DestructionEvent.fwd.hhForward declaration for core::pose::signals::DestructionEvent
src/core/pose/signals/DestructionEvent.hhSignal that the Pose is getting destroyed
src/core/pose/signals/EnergyEvent.fwd.hhForward declaration for core::pose::signals::EnergyEvent
src/core/pose/signals/EnergyEvent.hhSignal for an energy change in a Pose
src/core/pose/signals/GeneralEvent.fwd.hhForward declaration for core::pose::signals::GeneralEvent
src/core/pose/signals/GeneralEvent.hhSignal for a general change in a Pose
src/core/pose/symmetry/util.cc
src/core/pose/symmetry/util.hhUtility functions for handling with symmetric conformations
src/core/scoring/AtomVDW.cc
src/core/scoring/AtomVDW.fwd.hh
src/core/scoring/AtomVDW.hh
src/core/scoring/CenHBPotential.cc
src/core/scoring/CenHBPotential.fwd.hh
src/core/scoring/CenHBPotential.hh
src/core/scoring/constants.hhCore::scoring package constants
src/core/scoring/ContextGraph.ccContext graph class
src/core/scoring/ContextGraph.fwd.hhContext graph class forward declaration
src/core/scoring/ContextGraph.hhContext graph class declaration
src/core/scoring/ContextGraphFactory.ccContext graph class factory implementation
src/core/scoring/ContextGraphFactory.fwd.hhContext graph class factory forward declaration
src/core/scoring/ContextGraphFactory.hhContext graph factory class declaration
src/core/scoring/ContextGraphTypes.hh
src/core/scoring/DenseEnergyContainer.fwd.hh
src/core/scoring/DenseEnergyContainer.hh
src/core/scoring/DerivVectorPair.fwd.hhClass for storing a pair of derivative vectors, f1 and f2, used in our internal-geometry minimization algorithm
src/core/scoring/DerivVectorPair.hhClass for storing a pair of derivative vectors, f1 and f2, used in our internal-geometry minimization algorithm
src/core/scoring/DockingScoreFunction.cc
src/core/scoring/DockingScoreFunction.fwd.hh
src/core/scoring/DockingScoreFunction.hh
src/core/scoring/Energies.ccEnergies class to store cached energies and track the residue neighbor relationships
src/core/scoring/Energies.fwd.hhEnergies forward declarations header
src/core/scoring/Energies.hhEnergies class
src/core/scoring/EnergiesCacheableDataType.hhEnum for the DataCache within the Energies class
src/core/scoring/EnergyGraph.ccEnergy graph class implementation
src/core/scoring/EnergyGraph.fwd.hhEnergy graph class forward declaration
src/core/scoring/EnergyGraph.hhEnergy graph class declaration
src/core/scoring/EnergyMap.ccVector of scores implementation
src/core/scoring/EnergyMap.fwd.hhVector of scores forward declaration
src/core/scoring/EnergyMap.hhVector of scores declaration
src/core/scoring/EnvPairPotential.cc
src/core/scoring/EnvPairPotential.fwd.hh
src/core/scoring/EnvPairPotential.hh
src/core/scoring/GenBornPotential.cc
src/core/scoring/GenBornPotential.fwd.hh
src/core/scoring/GenBornPotential.hh
src/core/scoring/interpolation_util.hh
src/core/scoring/LREnergyContainer.cc
src/core/scoring/LREnergyContainer.fwd.hh
src/core/scoring/LREnergyContainer.hh
src/core/scoring/Membrane_FAPotential.cc
src/core/scoring/Membrane_FAPotential.fwd.hh
src/core/scoring/Membrane_FAPotential.hh
src/core/scoring/MembranePotential.cc
src/core/scoring/MembranePotential.fwd.hh
src/core/scoring/MembranePotential.hh
src/core/scoring/MembraneTopology.cc
src/core/scoring/MembraneTopology.fwd.hh
src/core/scoring/MembraneTopology.hh
src/core/scoring/MinimizationData.ccA container class for use by certain EnergyMethods during derivative and
src/core/scoring/MinimizationData.fwd.hhForward declaration of the container class for use by certain EnergyMethods
src/core/scoring/MinimizationData.hhA container class for use by certain EnergyMethods during derivative and
src/core/scoring/MinimizationGraph.ccMinimization graph class implementation
src/core/scoring/MinimizationGraph.fwd.hhMinimization graph class forward declaration
src/core/scoring/MinimizationGraph.hhMinimization graph class declaration
src/core/scoring/NeighborList.cc
src/core/scoring/NeighborList.fwd.hhFoward declaration of NeighborList class and owning pointer typedefs
src/core/scoring/NeighborList.hh
src/core/scoring/NeighborList.tmpl.hh
src/core/scoring/OmegaTether.ccOmegaTether potential class implementation
src/core/scoring/OmegaTether.fwd.hhOmega Tether potential class forward delcaration
src/core/scoring/OmegaTether.hhOmegaTether potential class delcaration
src/core/scoring/OneToAllEnergyContainer.fwd.hh
src/core/scoring/OneToAllEnergyContainer.hhA container interface for storing and scoring long range energies
src/core/scoring/P_AA.ccAmino acid probability arrays and functions
src/core/scoring/P_AA.fwd.hh
src/core/scoring/P_AA.hhAmino acid probability arrays and functions
src/core/scoring/PairEPotential.ccPairE knowledge-based potential class
src/core/scoring/PairEPotential.fwd.hhPairE knowledge-based potential class forward delcaration
src/core/scoring/PairEPotential.hh
src/core/scoring/PeptideBondedEnergyContainer.fwd.hh
src/core/scoring/PeptideBondedEnergyContainer.hhA container interface long range energies for n->n+1 interactions only
src/core/scoring/PoissonBoltzmannPotential.ccPoissonBoltzmann potential class implementation
src/core/scoring/PoissonBoltzmannPotential.fwd.hhPoissonBoltzmann potential class forward delcaration
src/core/scoring/PoissonBoltzmannPotential.hhPoisson Boltzmann potential class delcaration
src/core/scoring/ProteinTorsion.hhRamachandran potential class delcaration
src/core/scoring/Ramachandran.ccRamachandran potential class implementation
src/core/scoring/Ramachandran.fwd.hhRamachandran potential class forward delcaration
src/core/scoring/Ramachandran.hhRamachandran potential class delcaration
src/core/scoring/Ramachandran2B.ccNeighbor Dependent Ramachandran potential class implementation
src/core/scoring/Ramachandran2B.fwd.hh
src/core/scoring/Ramachandran2B.hh
src/core/scoring/ResidualDipolarCoupling.ccUses NMR RDC for scoring
src/core/scoring/ResidualDipolarCoupling.fwd.hh
src/core/scoring/ResidualDipolarCoupling.hhUses NMR RDC for scoring
src/core/scoring/ResidualDipolarCoupling_Rohl.ccUses NMR RDC for scoring
src/core/scoring/ResidualDipolarCoupling_Rohl.fwd.hh
src/core/scoring/ResidualDipolarCoupling_Rohl.hh
src/core/scoring/ResidueNeighborList.cc
src/core/scoring/ResidueNeighborList.fwd.hhForward declaration of a container class for use by the Etable and HackElec classes for storing residue-pair level atom-neighbor information
src/core/scoring/ResidueNeighborList.hhA container class for use by the Etable and HackElec classes for storing lists of atom neighbors
src/core/scoring/rms_util.ccRMS stuff from rosetta++
src/core/scoring/rms_util.hh
src/core/scoring/rms_util.tmpl.hh
src/core/scoring/sasa.ccRoutines which calculate solvent accessible surface area
src/core/scoring/sasa.hhRoutines which calculate solvent accessible surface area
src/core/scoring/ScoreFunction.ccScoreFunction class definition
src/core/scoring/ScoreFunction.fwd.hhCore::scoring::ScoreFunction forward declarations
src/core/scoring/ScoreFunction.hhScore function class
src/core/scoring/ScoreFunctionFactory.cc
src/core/scoring/ScoreFunctionFactory.hh
src/core/scoring/ScoreFunctionInfo.ccScore function class descriptor
src/core/scoring/ScoreFunctionInfo.fwd.hh
src/core/scoring/ScoreFunctionInfo.hh
src/core/scoring/ScoreFunctionParameter.hh
src/core/scoring/ScoreFunctionVariant.hh
src/core/scoring/ScoreType.cc
src/core/scoring/ScoreType.hhScore type enumeration
src/core/scoring/ScoreTypeManager.cc
src/core/scoring/ScoreTypeManager.hhScore type enumeration
src/core/scoring/ScoringManager.ccScoring manager class
src/core/scoring/ScoringManager.fwd.hh
src/core/scoring/ScoringManager.hhScoring manager class header
src/core/scoring/SecondaryStructurePotential.ccScoring manager class header
src/core/scoring/SecondaryStructurePotential.fwd.hh
src/core/scoring/SecondaryStructurePotential.hh
src/core/scoring/SecondaryStructureWeights.cc
src/core/scoring/SecondaryStructureWeights.hh
src/core/scoring/SmoothEnvPairPotential.cc
src/core/scoring/SmoothEnvPairPotential.fwd.hh
src/core/scoring/SmoothEnvPairPotential.hh
src/core/scoring/SS_Info.cc
src/core/scoring/SS_Info.fwd.hhData cache forward declarations for the secondary-structure based scores
src/core/scoring/SS_Info.hh
src/core/scoring/SS_Killhairpins_Info.cc
src/core/scoring/SS_Killhairpins_Info.fwd.hh
src/core/scoring/SS_Killhairpins_Info.hhScoring manager class header
src/core/scoring/TenANeighborGraph.ccNeighbor graph to represent for each residue the number of other residues within 10 Angstroms
src/core/scoring/TenANeighborGraph.fwd.hhTen Angstrom Neighbor graph class forward declaration
src/core/scoring/TenANeighborGraph.hhTen Angstrom Neighbor Graph class declaration
src/core/scoring/TwelveANeighborGraph.ccNeighbor graph to represent for each residue the number of other residues within 12 Angstroms
src/core/scoring/TwelveANeighborGraph.fwd.hhTwelve Angstrom Neighbor graph class forward declaration
src/core/scoring/TwelveANeighborGraph.hhTwelve Angstrom Neighbor Graph class declaration
src/core/scoring/types.hhCore::scoring package type declarations
src/core/scoring/UnfoldedStatePotential.ccUnfolded state energies based on energies of residues in fragments, definition file
src/core/scoring/UnfoldedStatePotential.fwd.hhUnfolded state energies based on energies of residues in fragments, forward declaration
src/core/scoring/UnfoldedStatePotential.hhUnfolded state energies based on energies of residues in fragments, declaration (header) file
src/core/scoring/util.ccNonmember functions for evaluating some or all energy methods on residues or residue pairs
src/core/scoring/util.hhNonmember functions for evaluating some or all energy methods on residues or residue pairs
src/core/scoring/WaterAdductHBondPotential.cc
src/core/scoring/WaterAdductHBondPotential.fwd.hh
src/core/scoring/WaterAdductHBondPotential.hh
src/core/scoring/carbon_hbonds/CarbonHBondEnergy.cc
src/core/scoring/carbon_hbonds/CarbonHBondEnergy.fwd.hhHydrogen bond energy method forward declaration
src/core/scoring/carbon_hbonds/CarbonHBondEnergy.hh
src/core/scoring/carbon_hbonds/CarbonHBondEnergyCreator.hhDeclaration for the class that connects CarbonHBondEnergy with the ScoringManager
src/core/scoring/carbon_hbonds/CarbonHBondPotential.cc
src/core/scoring/carbon_hbonds/CarbonHBondPotential.fwd.hh
src/core/scoring/carbon_hbonds/CarbonHBondPotential.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/constraints/AmbiguousConstraint.ccDeclarations for a type of constraint that holds a number of constraints
src/core/scoring/constraints/AmbiguousConstraint.fwd.hh
src/core/scoring/constraints/AmbiguousConstraint.hhDeclarations for a type of constraint that holds multiple other
src/core/scoring/constraints/AmbiguousNMRConstraint.ccDeclarations for a type of constraint that holds a number of constraints
src/core/scoring/constraints/AmbiguousNMRConstraint.fwd.hh
src/core/scoring/constraints/AmbiguousNMRConstraint.hhDeclarations for a type of constraint that holds multiple other constrains that belong to each other and are all evaluate at once
src/core/scoring/constraints/AmbiguousNMRDistanceConstraint.cc
src/core/scoring/constraints/AmbiguousNMRDistanceConstraint.fwd.hh
src/core/scoring/constraints/AmbiguousNMRDistanceConstraint.hh
src/core/scoring/constraints/AngleConstraint.ccDefinition of AngularConstraints
src/core/scoring/constraints/AngleConstraint.hh
src/core/scoring/constraints/AtomPairConstraint.cc
src/core/scoring/constraints/AtomPairConstraint.fwd.hh
src/core/scoring/constraints/AtomPairConstraint.hh
src/core/scoring/constraints/BackboneStubConstraint.cc
src/core/scoring/constraints/BackboneStubConstraint.fwd.hh
src/core/scoring/constraints/BackboneStubConstraint.hh
src/core/scoring/constraints/BasicConstraintCreators.cc
src/core/scoring/constraints/BasicConstraintCreators.hh
src/core/scoring/constraints/BigBinConstraint.cc
src/core/scoring/constraints/BigBinConstraint.hh
src/core/scoring/constraints/BoundConstraint.cc
src/core/scoring/constraints/BoundConstraint.fwd.hh
src/core/scoring/constraints/BoundConstraint.hh
src/core/scoring/constraints/CharmmPeriodicFunc.ccDefinition for periodic functions
src/core/scoring/constraints/CharmmPeriodicFunc.hhDefinition for a periodic function used in constraints
src/core/scoring/constraints/CircularGeneral1D_Func.ccA general 1D function that can be initialized by FArray or from text file. There's stuff like this all over Rosetta
src/core/scoring/constraints/CircularGeneral1D_Func.fwd.hhForward declaration for CircularGeneral1D_Func class
src/core/scoring/constraints/CircularGeneral1D_Func.hhA general 1D function that can be initialized by FArray or from text file. There's stuff like this all over Rosetta
src/core/scoring/constraints/CircularHarmonicFunc.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/CircularHarmonicFunc.fwd.hhForward declaration for CircularHarmonicFunc class
src/core/scoring/constraints/CircularHarmonicFunc.hh
src/core/scoring/constraints/CircularPowerFunc.cc
src/core/scoring/constraints/CircularPowerFunc.fwd.hhForward declaration for CircularPowerFunc class
src/core/scoring/constraints/CircularPowerFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/CircularSigmoidalFunc.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/CircularSigmoidalFunc.fwd.hhForward declaration for CircularSigmoidalFunc class
src/core/scoring/constraints/CircularSigmoidalFunc.hh
src/core/scoring/constraints/ConstantConstraint.cc
src/core/scoring/constraints/ConstantConstraint.hh
src/core/scoring/constraints/ConstantFunc.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/ConstantFunc.fwd.hhForward declaration for Constant functions
src/core/scoring/constraints/ConstantFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/Constraint.cc
src/core/scoring/constraints/Constraint.fwd.hh
src/core/scoring/constraints/Constraint.hhBase class definition for Constraint class hierarchy
src/core/scoring/constraints/ConstraintCreator.cc
src/core/scoring/constraints/ConstraintCreator.fwd.hh
src/core/scoring/constraints/ConstraintCreator.hhBase class for ConstraintCreators for the Constraint load-time factory registration scheme
src/core/scoring/constraints/ConstraintEnergyContainer.cc
src/core/scoring/constraints/ConstraintEnergyContainer.fwd.hh
src/core/scoring/constraints/ConstraintEnergyContainer.hh
src/core/scoring/constraints/ConstraintFactory.ccFactory for creating various types of constraints
src/core/scoring/constraints/ConstraintFactory.hhFactory for creating various types of constraints
src/core/scoring/constraints/ConstraintGraph.cc
src/core/scoring/constraints/ConstraintGraph.fwd.hhConstraints Energy Graph class forward declaration
src/core/scoring/constraints/ConstraintGraph.hh
src/core/scoring/constraints/ConstraintIO.cc
src/core/scoring/constraints/ConstraintIO.hh
src/core/scoring/constraints/Constraints.cc
src/core/scoring/constraints/Constraints.fwd.hh
src/core/scoring/constraints/Constraints.hh
src/core/scoring/constraints/ConstraintsEnergy.cc
src/core/scoring/constraints/ConstraintsEnergy.fwd.hhConstraints Energy Method forward declaration
src/core/scoring/constraints/ConstraintsEnergy.hhConstraints Energy Method declaration
src/core/scoring/constraints/ConstraintsEnergyCreator.hhDeclaration for the class that connects ConstraintsEnergy with the ScoringManager
src/core/scoring/constraints/ConstraintSet.cc
src/core/scoring/constraints/ConstraintSet.fwd.hh
src/core/scoring/constraints/ConstraintSet.hh
src/core/scoring/constraints/CoordinateConstraint.cc
src/core/scoring/constraints/CoordinateConstraint.hh
src/core/scoring/constraints/CountViolFunc.ccWeighted constraint function that reweights other constraints by a constant scalar value
src/core/scoring/constraints/CountViolFunc.hh
src/core/scoring/constraints/CstMinimizationData.hhA cacheable data wrapper for ConstraintsOPs for use in minimization
src/core/scoring/constraints/DihedralConstraint.cc
src/core/scoring/constraints/DihedralConstraint.fwd.hh
src/core/scoring/constraints/DihedralConstraint.hh
src/core/scoring/constraints/DihedralPairConstraint.cc
src/core/scoring/constraints/DihedralPairConstraint.hh
src/core/scoring/constraints/DOF_Constraint.fwd.hh
src/core/scoring/constraints/DOF_Constraint.hh
src/core/scoring/constraints/EtableFunc.cc
src/core/scoring/constraints/EtableFunc.fwd.hhForward declaration for Etable functions
src/core/scoring/constraints/EtableFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/FadeFunc.cc
src/core/scoring/constraints/FadeFunc.fwd.hhForward declaration for Mixture functions
src/core/scoring/constraints/FadeFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/FlatHarmonicFunc.cc
src/core/scoring/constraints/FlatHarmonicFunc.fwd.hhForward declaration for Mixture functions
src/core/scoring/constraints/FlatHarmonicFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/FourPointsFunc.cc
src/core/scoring/constraints/FourPointsFunc.fwd.hh
src/core/scoring/constraints/FourPointsFunc.hh
src/core/scoring/constraints/Func.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/Func.fwd.hh
src/core/scoring/constraints/Func.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/FuncFactory.ccFactory for creating various types of constraints
src/core/scoring/constraints/FuncFactory.fwd.hhFactory for creating various types of constraints
src/core/scoring/constraints/FuncFactory.hhFactory for creating various types of constraints
src/core/scoring/constraints/GaussianFunc.cc
src/core/scoring/constraints/GaussianFunc.fwd.hhForward declaration for Gaussian functions
src/core/scoring/constraints/GaussianFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/HarmonicFunc.cc
src/core/scoring/constraints/HarmonicFunc.fwd.hhForward declaration for Mixture functions
src/core/scoring/constraints/HarmonicFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/IdentityFunc.cc
src/core/scoring/constraints/IdentityFunc.fwd.hhForward declaration for Identity function
src/core/scoring/constraints/IdentityFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/KarplusFunc.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/KarplusFunc.fwd.hh
src/core/scoring/constraints/KarplusFunc.hh
src/core/scoring/constraints/KofNConstraint.ccMeta constraint where N constraints declared
src/core/scoring/constraints/KofNConstraint.fwd.hhMeta constraint where N constraints declared
src/core/scoring/constraints/KofNConstraint.hhMeta constraint where N constraints declared
src/core/scoring/constraints/LinearPenaltyFunction.cc
src/core/scoring/constraints/LinearPenaltyFunction.hhLinear penalty for values outside a certain range
src/core/scoring/constraints/LocalCoordinateConstraint.cc
src/core/scoring/constraints/LocalCoordinateConstraint.hh
src/core/scoring/constraints/MinMultiHarmonicFunc.cc
src/core/scoring/constraints/MinMultiHarmonicFunc.fwd.hhForward declaration for Mixture functions
src/core/scoring/constraints/MinMultiHarmonicFunc.hh
src/core/scoring/constraints/MixtureFunc.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/MixtureFunc.fwd.hhForward declaration for Mixture functions
src/core/scoring/constraints/MixtureFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/MultiConstraint.ccDeclarations for a type of constraint that holds multiple other constrains that belong to each other and are all evaluate at once
src/core/scoring/constraints/MultiConstraint.fwd.hh
src/core/scoring/constraints/MultiConstraint.hhDeclarations for a type of constraint that holds multiple other constrains that belong to each other and are all evaluate at once
src/core/scoring/constraints/NamedAtomPairConstraint.cc
src/core/scoring/constraints/NamedAtomPairConstraint.fwd.hh
src/core/scoring/constraints/NamedAtomPairConstraint.hh
src/core/scoring/constraints/NonResidueTypeConstraint.cc
src/core/scoring/constraints/NonResidueTypeConstraint.fwd.hh
src/core/scoring/constraints/NonResidueTypeConstraint.hh
src/core/scoring/constraints/PeriodicFunc.ccDefinition for periodic functions
src/core/scoring/constraints/PeriodicFunc.hhDefinition for a periodic function used in constraints
src/core/scoring/constraints/ResidueTypeConstraint.cc
src/core/scoring/constraints/ResidueTypeConstraint.fwd.hh
src/core/scoring/constraints/ResidueTypeConstraint.hh
src/core/scoring/constraints/ResidueTypeLinkingConstraint.cc
src/core/scoring/constraints/ResidueTypeLinkingConstraint.fwd.hhConstrainting two residues to be the same type, based on
src/core/scoring/constraints/ResidueTypeLinkingConstraint.hh
src/core/scoring/constraints/ScalarWeightedFunc.ccWeighted constraint function that reweights other constraints by a constant scalar value
src/core/scoring/constraints/ScalarWeightedFunc.fwd.hh
src/core/scoring/constraints/ScalarWeightedFunc.hhWeighted constraint function that encapsulates other constraints
src/core/scoring/constraints/SequenceProfileConstraint.ccThis is a constraint that refers to a core::sequence::SequenceProfile? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design). A note about the SequenceProfile::read_from_checkpoint function that is used to read in scores for amino acid types: the first line of the file will be ignored
src/core/scoring/constraints/SequenceProfileConstraint.fwd.hh
src/core/scoring/constraints/SequenceProfileConstraint.hhThis is a constraint that refers to a core::sequence::SequenceProfile? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design)
src/core/scoring/constraints/SequenceProfileConstraintCreator.hh
src/core/scoring/constraints/SigmoidFunc.cc
src/core/scoring/constraints/SigmoidFunc.fwd.hh
src/core/scoring/constraints/SigmoidFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/SiteConstraint.ccThis class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints
src/core/scoring/constraints/SiteConstraint.fwd.hhThis class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints
src/core/scoring/constraints/SiteConstraint.hhThis class is an AmbiguousConstraint in which the set is comprised of AtomPairConstraints
src/core/scoring/constraints/SkipViolFunc.ccWeighted constraint function that reweights other constraints by a constant scalar value
src/core/scoring/constraints/SkipViolFunc.hh
src/core/scoring/constraints/SoedingFunc.cc
src/core/scoring/constraints/SoedingFunc.fwd.hhForward declaration for SoedingFunc class
src/core/scoring/constraints/SoedingFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/SOGFunc.cc
src/core/scoring/constraints/SOGFunc.fwd.hhForward declaration for SOG functions
src/core/scoring/constraints/SOGFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/SOGFunc_Impl.ccDefinition for functions used in definition of constraints
src/core/scoring/constraints/SOGFunc_Impl.fwd.hhForward declaration for SOG functions
src/core/scoring/constraints/SOGFunc_Impl.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/SplineFunc.ccConstraint function for looking up data in a histogram over which a spline is created
src/core/scoring/constraints/SplineFunc.fwd.hhForward declaration for SplineFunc
src/core/scoring/constraints/SplineFunc.hhConstraint function for looking up data in a histogram over which a spline is created
src/core/scoring/constraints/SquareWellFunc.cc
src/core/scoring/constraints/SquareWellFunc.fwd.hhForward declaration for Mixture functions
src/core/scoring/constraints/SquareWellFunc.hhDefinition for functions used in definition of constraints
src/core/scoring/constraints/SumFunc.ccWeighted constraint function that reweights other constraints by a constant scalar value
src/core/scoring/constraints/SumFunc.fwd.hh
src/core/scoring/constraints/SumFunc.hhSum of several individual constraints
src/core/scoring/constraints/TopOutFunc.cc
src/core/scoring/constraints/TopOutFunc.fwd.hhImplementation of phenix "top-out" function
src/core/scoring/constraints/TopOutFunc.hhImplementation of phenix "top-out" function Similar to Geman-McClure: harmonic near 'x0_', flat past 'limit_'
src/core/scoring/constraints/util.ccUtility functions for defining constraints. Maybe better placed in src/numeric?
src/core/scoring/constraints/util.hhUtility functions for defining constraints. Maybe better placed in src/numeric?
src/core/scoring/constraints/XYZ_Func.cc
src/core/scoring/constraints/XYZ_Func.fwd.hh
src/core/scoring/constraints/XYZ_Func.hh
src/core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergy.cc
src/core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergy.fwd.hhClass declaration
src/core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergy.hh
src/core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergyCreator.hhDeclaration for the class that connects FullatomCustomPairDistanceEnergy with the ScoringManager
src/core/scoring/disulfides/CentroidDisulfideEnergy.ccCentroid Disulfide Energy class implementation
src/core/scoring/disulfides/CentroidDisulfideEnergy.fwd.hhCentroid Disulfide Energy class forward declaration
src/core/scoring/disulfides/CentroidDisulfideEnergy.hhCentroid Disulfide Energy class declaration
src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.cc
src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.fwd.hh
src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.hhDisulfide Energy Container class declaration
src/core/scoring/disulfides/CentroidDisulfideEnergyCreator.hhDeclaration for the class that connects CentroidDisulfideEnergy with the ScoringManager
src/core/scoring/disulfides/CentroidDisulfidePotential.ccCentroid Disulfide Energy Potentials
src/core/scoring/disulfides/CentroidDisulfidePotential.fwd.hh
src/core/scoring/disulfides/CentroidDisulfidePotential.hhCentroid Disulfide Energy Potentials
src/core/scoring/disulfides/DisulfideAtomIndices.ccDisulfide Energy class implementation
src/core/scoring/disulfides/DisulfideAtomIndices.fwd.hhDisulfide Atom Indices class forward declaration
src/core/scoring/disulfides/DisulfideAtomIndices.hhDisulfide Atom Indices class declaration
src/core/scoring/disulfides/DisulfideMatchingDatabase.cc
src/core/scoring/disulfides/DisulfideMatchingDatabase.hhCentroid Disulfide Energy Databases
src/core/scoring/disulfides/DisulfideMatchingEnergy.ccCentroid Disulfide Energy class implementation
src/core/scoring/disulfides/DisulfideMatchingEnergy.fwd.hhCentroid Disulfide Energy class forward declaration
src/core/scoring/disulfides/DisulfideMatchingEnergy.hhCentroid Disulfide Energy class declaration
src/core/scoring/disulfides/DisulfideMatchingEnergyContainer.cc
src/core/scoring/disulfides/DisulfideMatchingEnergyContainer.fwd.hh
src/core/scoring/disulfides/DisulfideMatchingEnergyContainer.hhDisulfide Energy Container class declaration
src/core/scoring/disulfides/DisulfideMatchingEnergyCreator.hhDeclaration for the class that connects DisulfideMatchingEnergy with the ScoringManager
src/core/scoring/disulfides/DisulfideMatchingPotential.cc
src/core/scoring/disulfides/DisulfideMatchingPotential.fwd.hh
src/core/scoring/disulfides/DisulfideMatchingPotential.hhCentroid Disulfide Energy Potentials
src/core/scoring/disulfides/FullatomDisulfideEnergy.ccDisulfide Energy class implementation
src/core/scoring/disulfides/FullatomDisulfideEnergy.fwd.hhDisulfide Energy class forward declaration
src/core/scoring/disulfides/FullatomDisulfideEnergy.hh
src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc
src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.fwd.hh
src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.hhDisulfide Energy Container class declaration
src/core/scoring/disulfides/FullatomDisulfideEnergyCreator.hhDeclaration for the class that connects FullatomDisulfideEnergy with the ScoringManager
src/core/scoring/disulfides/FullatomDisulfidePotential.ccFullatom Disulfide potential class definition
src/core/scoring/disulfides/FullatomDisulfidePotential.fwd.hhFullatom Disulfide Potential class forward declaration
src/core/scoring/disulfides/FullatomDisulfidePotential.hhFullatom Disulfide Potential class declaration
src/core/scoring/dna/base_geometry.cc
src/core/scoring/dna/base_geometry.hh
src/core/scoring/dna/BasePartner.cc
src/core/scoring/dna/BasePartner.fwd.hh
src/core/scoring/dna/BasePartner.hh
src/core/scoring/dna/DirectReadoutPotential.cc
src/core/scoring/dna/DirectReadoutPotential.fwd.hh
src/core/scoring/dna/DirectReadoutPotential.hh
src/core/scoring/dna/DNA_BasePotential.cc
src/core/scoring/dna/DNA_BasePotential.fwd.hh
src/core/scoring/dna/DNA_BasePotential.hh
src/core/scoring/dna/scoring.hh
src/core/scoring/dna/setup.cc
src/core/scoring/dna/setup.hh
src/core/scoring/dssp/Dssp.cc
src/core/scoring/dssp/Dssp.fwd.hhFwd headers for ns dssp
src/core/scoring/dssp/Dssp.hh
src/core/scoring/dssp/PairingsList.cc
src/core/scoring/dssp/PairingsList.fwd.hhFwd headers for ns dssp
src/core/scoring/dssp/PairingsList.hh
src/core/scoring/dssp/StrandPairing.cc
src/core/scoring/dssp/StrandPairing.fwd.hh
src/core/scoring/dssp/StrandPairing.hh
src/core/scoring/dssp/util.cc
src/core/scoring/dssp/util.hh
src/core/scoring/electron_density/ElecDensAllAtomCenEnergy.cc
src/core/scoring/electron_density/ElecDensAllAtomCenEnergy.hh
src/core/scoring/electron_density/ElecDensAllAtomCenEnergyCreator.hhDeclaration for the class that connects ElecDensAllAtomCenEnergy with the ScoringManager
src/core/scoring/electron_density/ElecDensCenEnergy.cc
src/core/scoring/electron_density/ElecDensCenEnergy.hh
src/core/scoring/electron_density/ElecDensCenEnergyCreator.hhDeclaration for the class that connects ElecDensCenEnergy with the ScoringManager
src/core/scoring/electron_density/ElecDensEnergies.fwd.hh
src/core/scoring/electron_density/ElecDensEnergy.cc
src/core/scoring/electron_density/ElecDensEnergy.hh
src/core/scoring/electron_density/ElecDensEnergyCreator.hhDeclaration for the class that connects ElecDensEnergy with the ScoringManager
src/core/scoring/electron_density/ElectronDensity.cc
src/core/scoring/electron_density/ElectronDensity.fwd.hh
src/core/scoring/electron_density/ElectronDensity.hh
src/core/scoring/electron_density/FastDensEnergy.cc
src/core/scoring/electron_density/FastDensEnergy.hh
src/core/scoring/electron_density/FastDensEnergyCreator.hhDeclaration for the class that connects FastDensEnergy with the ScoringManager
src/core/scoring/electron_density/PattersonCorrEnergy.cc
src/core/scoring/electron_density/PattersonCorrEnergy.hhScoring a structure's fit to a patterson map
src/core/scoring/electron_density/PattersonCorrEnergyCreator.hhDeclaration for the class that connects PattersonCorrEnergy with the ScoringManager
src/core/scoring/electron_density/SplineInterp.cc
src/core/scoring/electron_density/SplineInterp.hh
src/core/scoring/electron_density/util.cc
src/core/scoring/electron_density/util.hh
src/core/scoring/electron_density/xray_scattering.cc
src/core/scoring/electron_density/xray_scattering.hh
src/core/scoring/electron_density_atomwise/ElecDensAtomwiseEnergy.ccElec_dens_atomwise scoring method implementation
src/core/scoring/electron_density_atomwise/ElecDensAtomwiseEnergy.fwd.hhElec_dens_atomwise energy method forward declaration
src/core/scoring/electron_density_atomwise/ElecDensAtomwiseEnergy.hhDeclaration for elec_dens_atomwise scoring method
src/core/scoring/electron_density_atomwise/ElecDensAtomwiseEnergyCreator.hh
src/core/scoring/electron_density_atomwise/ElectronDensityAtomwise.ccElec_dens_atomwise scoring method implementation
src/core/scoring/electron_density_atomwise/ElectronDensityAtomwise.hhScoring a structure against an electron density map
src/core/scoring/etable/atom_pair_energy_inline.hh
src/core/scoring/etable/BaseEtableEnergy.hh
src/core/scoring/etable/BaseEtableEnergy.tmpl.hh
src/core/scoring/etable/BaseMembEtableEnergy.hh
src/core/scoring/etable/CoarseEtableEnergy.cc
src/core/scoring/etable/CoarseEtableEnergy.fwd.hh
src/core/scoring/etable/CoarseEtableEnergy.hh
src/core/scoring/etable/CoarseEtableEnergyCreator.hhDeclaration for the class that connects CoarseEtableEnergy with the ScoringManager
src/core/scoring/etable/Etable.cc
src/core/scoring/etable/Etable.fwd.hh
src/core/scoring/etable/Etable.hh
src/core/scoring/etable/EtableEnergy.ccAtom pair energy functions
src/core/scoring/etable/EtableEnergy.fwd.hh
src/core/scoring/etable/EtableEnergy.hhEtable energy method class declaration
src/core/scoring/etable/EtableEnergyCreator.hhDeclaration for the class that connects EtableEnergy with the ScoringManager
src/core/scoring/etable/EtableOptions.cc
src/core/scoring/etable/EtableOptions.hh
src/core/scoring/etable/MembEtable.cc
src/core/scoring/etable/MembEtable.fwd.hh
src/core/scoring/etable/MembEtable.hh
src/core/scoring/etable/count_pair/CountPair1B.cc
src/core/scoring/etable/count_pair/CountPair1B.fwd.hhCount pair for residue pairs connected with one bond
src/core/scoring/etable/count_pair/CountPair1B.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds
src/core/scoring/etable/count_pair/CountPairAll.ccCount pair for residues where all atom pairs should be counted
src/core/scoring/etable/count_pair/CountPairAll.fwd.hhCount pair for residues where all atom pairs should be counted
src/core/scoring/etable/count_pair/CountPairAll.hhCount pair for residues where all atom pairs should be counted
src/core/scoring/etable/count_pair/CountPairCrossover3.cc
src/core/scoring/etable/count_pair/CountPairCrossover3.fwd.hh
src/core/scoring/etable/count_pair/CountPairCrossover3.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds
src/core/scoring/etable/count_pair/CountPairCrossover4.ccCount pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 4 bonds
src/core/scoring/etable/count_pair/CountPairCrossover4.fwd.hhCount pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 4 bonds
src/core/scoring/etable/count_pair/CountPairCrossover4.hhCount pair for residue pairs where the crossover from excluding to counting atom pair interactions is at 4 bonds
src/core/scoring/etable/count_pair/CountPairFactory.cc
src/core/scoring/etable/count_pair/CountPairFactory.fwd.hh
src/core/scoring/etable/count_pair/CountPairFactory.hh
src/core/scoring/etable/count_pair/CountPairFunction.ccCount pair base class implementation
src/core/scoring/etable/count_pair/CountPairFunction.fwd.hhCount pair base class forward declaration
src/core/scoring/etable/count_pair/CountPairFunction.hhCount pair base class interface
src/core/scoring/etable/count_pair/CountPairGeneric.cc
src/core/scoring/etable/count_pair/CountPairGeneric.fwd.hh
src/core/scoring/etable/count_pair/CountPairGeneric.hh
src/core/scoring/etable/count_pair/CountPairIntraRes.cc
src/core/scoring/etable/count_pair/CountPairIntraRes.fwd.hh
src/core/scoring/etable/count_pair/CountPairIntraRes.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds
src/core/scoring/etable/count_pair/CountPairIntraResC3.ccCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds
src/core/scoring/etable/count_pair/CountPairIntraResC3.fwd.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds
src/core/scoring/etable/count_pair/CountPairIntraResC3.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 3 bonds
src/core/scoring/etable/count_pair/CountPairIntraResC4.ccCount pair for intra-residue LJ/LK, where the crossover from excluding to counting atom pair interactions is at 4 bonds
src/core/scoring/etable/count_pair/CountPairIntraResC4.fwd.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 4 bonds
src/core/scoring/etable/count_pair/CountPairIntraResC4.hhCount pair for residue pairs connected with one bond, where the crossover from excluding to counting atom pair interactions is at 4 bonds
src/core/scoring/etable/count_pair/CountPairNone.ccCount pair for residues where all atom pairs should be counted
src/core/scoring/etable/count_pair/CountPairNone.fwd.hhCount pair for residues where all atom pairs should be counted
src/core/scoring/etable/count_pair/CountPairNone.hhCount pair for residues where all atom pairs should be counted
src/core/scoring/etable/count_pair/types.hh
src/core/scoring/etable/etrie/CountPairData_1_1.ccCountPair Data for a residue with one connection point
src/core/scoring/etable/etrie/CountPairData_1_1.fwd.hh
src/core/scoring/etable/etrie/CountPairData_1_1.hh
src/core/scoring/etable/etrie/CountPairData_1_2.cc
src/core/scoring/etable/etrie/CountPairData_1_2.fwd.hh
src/core/scoring/etable/etrie/CountPairData_1_2.hh
src/core/scoring/etable/etrie/CountPairData_1_3.cc
src/core/scoring/etable/etrie/CountPairData_1_3.fwd.hh
src/core/scoring/etable/etrie/CountPairData_1_3.hh
src/core/scoring/etable/etrie/CountPairDataGeneric.cc
src/core/scoring/etable/etrie/CountPairDataGeneric.fwd.hhForward declaration of generic count-pair data class for the trie
src/core/scoring/etable/etrie/CountPairDataGeneric.hhClass to hold per-atom count pair for residues with non-canonical inter-residue connections
src/core/scoring/etable/etrie/EtableAtom.cc
src/core/scoring/etable/etrie/EtableAtom.fwd.hh
src/core/scoring/etable/etrie/EtableAtom.hh
src/core/scoring/etable/etrie/EtableTrie.fwd.hh
src/core/scoring/etable/etrie/TrieCountPair1BC3.cc
src/core/scoring/etable/etrie/TrieCountPair1BC3.fwd.hh
src/core/scoring/etable/etrie/TrieCountPair1BC3.hh
src/core/scoring/etable/etrie/TrieCountPair1BC4.cc
src/core/scoring/etable/etrie/TrieCountPair1BC4.fwd.hh
src/core/scoring/etable/etrie/TrieCountPair1BC4.hh
src/core/scoring/etable/etrie/TrieCountPairAll.cc
src/core/scoring/etable/etrie/TrieCountPairAll.fwd.hh
src/core/scoring/etable/etrie/TrieCountPairAll.hh
src/core/scoring/etable/etrie/TrieCountPairGeneric.cc
src/core/scoring/etable/etrie/TrieCountPairGeneric.fwd.hh
src/core/scoring/etable/etrie/TrieCountPairGeneric.hhImplementation of count pair class to go along with the CountPairGeneric atom data
src/core/scoring/etable/etrie/TrieCountPairNone.cc
src/core/scoring/etable/etrie/TrieCountPairNone.fwd.hh
src/core/scoring/etable/etrie/TrieCountPairNone.hh
src/core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergy.cc
src/core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergy.fwd.hh
src/core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergy.hh
src/core/scoring/geometric_solvation/ContextIndependentGeometricSolEnergyCreator.hh
src/core/scoring/geometric_solvation/DatabaseOccSolEne.ccDatabase containing params for OccludedHbondSolEnergy
src/core/scoring/geometric_solvation/DatabaseOccSolEne.fwd.hhDatabase containing params for OccludedHbondSolEnergy
src/core/scoring/geometric_solvation/DatabaseOccSolEne.hhDatabase containing params for OccludedHbondSolEnergy
src/core/scoring/geometric_solvation/ExactOccludedHbondSolEnergy.cc
src/core/scoring/geometric_solvation/ExactOccludedHbondSolEnergy.hhSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/ExactOccludedHbondSolEnergyCreator.hhDeclaration for the class that connects ExactOccludedHbondSolEnergy with the ScoringManager
src/core/scoring/geometric_solvation/GeometricSolEnergy.cc
src/core/scoring/geometric_solvation/GeometricSolEnergy.fwd.hh
src/core/scoring/geometric_solvation/GeometricSolEnergy.hh
src/core/scoring/geometric_solvation/GeometricSolEnergyCreator.hhDeclaration for the class that connects GeometricSolEnergy with the ScoringManager
src/core/scoring/geometric_solvation/non_scorefxn_exact_model.cc
src/core/scoring/geometric_solvation/non_scorefxn_exact_model.hh
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy.ccSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy.fwd.hhSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy.hhSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy_onebody.ccSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy_onebody.fwd.hhSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy_onebody.hhSolvation model based on penalizing potential for Hbonding to solvent
src/core/scoring/geometric_solvation/OccludedHbondSolEnergy_onebodyCreator.hhDeclaration for the class that connects OccludedHbondSolEnergy_onebody with the ScoringManager
src/core/scoring/geometric_solvation/OccludedHbondSolEnergyCreator.hhDeclaration for the class that connects OccludedHbondSolEnergy with the ScoringManager
src/core/scoring/hackaro/HackAroEnergy.cc
src/core/scoring/hackaro/HackAroEnergy.fwd.hh
src/core/scoring/hackaro/HackAroEnergy.hh
src/core/scoring/hackaro/HackAroEnergyCreator.hh
src/core/scoring/hackelec/ElecAtom.cc
src/core/scoring/hackelec/ElecAtom.fwd.hh
src/core/scoring/hackelec/ElecAtom.hh
src/core/scoring/hackelec/HackElecEnergy.cc
src/core/scoring/hackelec/HackElecEnergy.fwd.hh
src/core/scoring/hackelec/HackElecEnergy.hh
src/core/scoring/hackelec/HackElecEnergyAroAll.ccElectrostatics energy method for aromatic side chain (stand-in for pi/pi interactions)
src/core/scoring/hackelec/HackElecEnergyAroAll.fwd.hhElectrostatics for RNA class forward declaration
src/core/scoring/hackelec/HackElecEnergyAroAll.hh
src/core/scoring/hackelec/HackElecEnergyAroAllCreator.hhDeclaration for the class that connects HackElecEnergyAroAll with the ScoringManager
src/core/scoring/hackelec/HackElecEnergyAroAro.ccElectrostatics energy method for aromatic side chain (stand-in for pi/pi interactions)
src/core/scoring/hackelec/HackElecEnergyAroAro.fwd.hhElectrostatics for RNA class forward declaration
src/core/scoring/hackelec/HackElecEnergyAroAro.hh
src/core/scoring/hackelec/HackElecEnergyAroAroCreator.hhDeclaration for the class that connects HackElecEnergyAroAro with the ScoringManager
src/core/scoring/hackelec/HackElecEnergyCreator.hhDeclaration for the class that connects HackElecEnergy with the ScoringManager
src/core/scoring/hackelec/RNAHackElecEnergy.ccElectrostatics energy method for RNA class implementation
src/core/scoring/hackelec/RNAHackElecEnergy.fwd.hhElectrostatics for RNA class forward declaration
src/core/scoring/hackelec/RNAHackElecEnergy.hh
src/core/scoring/hackelec/RNAHackElecEnergyCreator.hhDeclaration for the class that connects RNAHackElecEnergy with the ScoringManager
src/core/scoring/hbonds/constants.hh
src/core/scoring/hbonds/FadeInterval.ccFadeInterval class, used a simplified cross term for the hbond score term
src/core/scoring/hbonds/FadeInterval.fwd.hh
src/core/scoring/hbonds/FadeInterval.hhFadeInterval class, used a simplified cross term for the hbond score term
src/core/scoring/hbonds/HBEvalTuple.cc
src/core/scoring/hbonds/HBEvalTuple.fwd.hhTuple describing data about the donor and acceptor in a single hbond
src/core/scoring/hbonds/HBEvalTuple.hhTuple describing data about the donor and acceptor in a single hbond
src/core/scoring/hbonds/HBondDatabase.cc
src/core/scoring/hbonds/HBondDatabase.fwd.hhForward header for HBondDatabase class
src/core/scoring/hbonds/HBondDatabase.hh
src/core/scoring/hbonds/HBondEnergy.cc
src/core/scoring/hbonds/HBondEnergy.fwd.hh
src/core/scoring/hbonds/HBondEnergy.hh
src/core/scoring/hbonds/HBondEnergyCreator.hhDeclaration for the class that connects HBondEnergy with the ScoringManager
src/core/scoring/hbonds/HBondOptions.ccHBondOptions class, holds the options for the hbond energy function
src/core/scoring/hbonds/HBondOptions.fwd.hhForward header for HBondOptions class
src/core/scoring/hbonds/HBondOptions.hhHBondOptions class, holds the options for the hbond energy function
src/core/scoring/hbonds/hbonds.cc
src/core/scoring/hbonds/hbonds.hh
src/core/scoring/hbonds/hbonds_geom.cc
src/core/scoring/hbonds/hbonds_geom.hh
src/core/scoring/hbonds/HBondSet.cc
src/core/scoring/hbonds/HBondSet.fwd.hhHydrogen bond set for a pose forward declaration
src/core/scoring/hbonds/HBondSet.hhHydrogen bond set class implementation
src/core/scoring/hbonds/HBondTypeManager.cc
src/core/scoring/hbonds/HBondTypeManager.fwd.hhForward header for HBondTypeManager class
src/core/scoring/hbonds/HBondTypeManager.hhHBond enumeration type manager
src/core/scoring/hbonds/polynomial.ccClasses for hydrogen bond polynomial evaluation functions
src/core/scoring/hbonds/polynomial.fwd.hhForward header for Polynomial class
src/core/scoring/hbonds/polynomial.hhPolynomial objects for hydrogen bond score term
src/core/scoring/hbonds/types.ccFunctions for manipulating hydrogen bond types
src/core/scoring/hbonds/types.hhCore::scoring package type declarations
src/core/scoring/hbonds/hbtrie/HBAtom.cc
src/core/scoring/hbonds/hbtrie/HBAtom.fwd.hh
src/core/scoring/hbonds/hbtrie/HBAtom.hh
src/core/scoring/hbonds/hbtrie/HBCountPairFunction.cc
src/core/scoring/hbonds/hbtrie/HBCountPairFunction.fwd.hh
src/core/scoring/hbonds/hbtrie/HBCountPairFunction.hh
src/core/scoring/hbonds/hbtrie/HBCPData.cc
src/core/scoring/hbonds/hbtrie/HBCPData.fwd.hh
src/core/scoring/hbonds/hbtrie/HBCPData.hhThis class enforces the sc/bb hbond exclusion rule for use in the trie
src/core/scoring/hbonds/hbtrie/HBondTrie.fwd.hh
src/core/scoring/interface/DDPlookup.cc
src/core/scoring/interface/DDPlookup.fwd.hh
src/core/scoring/interface/DDPlookup.hh
src/core/scoring/interface/DDPscore.cc
src/core/scoring/interface/DDPscore.fwd.hh
src/core/scoring/interface/DDPscore.hh
src/core/scoring/interface/DDPscoreCreator.hh
src/core/scoring/memb_etable/BaseMembEtableEnergy.hh
src/core/scoring/memb_etable/MembEtable.cc
src/core/scoring/memb_etable/MembEtable.fwd.hh
src/core/scoring/memb_etable/MembEtable.hh
src/core/scoring/methods/BurialEnergy.cc
src/core/scoring/methods/BurialEnergy.hhEnergy term use for scoring predicted burial
src/core/scoring/methods/BurialEnergyCreator.hhDeclaration for the class that connects BurialEnergy with the ScoringManager
src/core/scoring/methods/CartesianBondedEnergy.cc
src/core/scoring/methods/CartesianBondedEnergy.fwd.hh
src/core/scoring/methods/CartesianBondedEnergy.hh
src/core/scoring/methods/CartesianBondedEnergyCreator.hhDeclaration for the class that connects CartesianBondedEnergy with the ScoringManager
src/core/scoring/methods/CenHBEnergy.ccSmooth, differentiable version of centroid hbond term
src/core/scoring/methods/CenHBEnergy.fwd.hh
src/core/scoring/methods/CenHBEnergy.hhSmooth, differentiable version of centroid hbond term
src/core/scoring/methods/CenHBEnergyCreator.hhDeclaration for the class that connects CenHBEnergy with the ScoringManager
src/core/scoring/methods/CenPairEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/CenPairEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/CenPairEnergyCreator.hh
src/core/scoring/methods/chainbreak_util.ccUtility functions for scoring chainbreaks
src/core/scoring/methods/chainbreak_util.hhUtility functions for scoring chainbreaks
src/core/scoring/methods/ChainbreakEnergy.cc
src/core/scoring/methods/ChainbreakEnergy.fwd.hh
src/core/scoring/methods/ChainbreakEnergy.hh
src/core/scoring/methods/ChainbreakEnergyCreator.hhDeclaration for the class that connects ChainbreakEnergy with the ScoringManager
src/core/scoring/methods/ContactOrderEnergy.ccCalculates the contact order of a given conformation average sequence
src/core/scoring/methods/ContactOrderEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/ContactOrderEnergyCreator.hhDeclaration for the class that connects ContactOrderEnergy with the ScoringManager
src/core/scoring/methods/ContextDependentLRTwoBodyEnergy.ccContext-Dependent, Long-Range, Two-Body Energy class implementation
src/core/scoring/methods/ContextDependentLRTwoBodyEnergy.fwd.hhContext-Dependent, Long-Range, Two-Body Energy Method class forward declaration
src/core/scoring/methods/ContextDependentLRTwoBodyEnergy.hh
src/core/scoring/methods/ContextDependentOneBodyEnergy.cc
src/core/scoring/methods/ContextDependentOneBodyEnergy.fwd.hh
src/core/scoring/methods/ContextDependentOneBodyEnergy.hh
src/core/scoring/methods/ContextDependentTwoBodyEnergy.ccScore function class
src/core/scoring/methods/ContextDependentTwoBodyEnergy.fwd.hhForward declaration for the Context-Dependent (ShortRange) Two-Body EnergyMethod base class
src/core/scoring/methods/ContextDependentTwoBodyEnergy.hh
src/core/scoring/methods/ContextIndependentLRTwoBodyEnergy.ccContext-Independent, Long-Range, Two-Body Energy class implementation
src/core/scoring/methods/ContextIndependentLRTwoBodyEnergy.fwd.hhContext-Independent, Long-Range, Two-Body Energy Method class forward declaration
src/core/scoring/methods/ContextIndependentLRTwoBodyEnergy.hhContext-Dependent, Long-Range, Two-Body Energy class declaration
src/core/scoring/methods/ContextIndependentOneBodyEnergy.cc
src/core/scoring/methods/ContextIndependentOneBodyEnergy.fwd.hh
src/core/scoring/methods/ContextIndependentOneBodyEnergy.hh
src/core/scoring/methods/ContextIndependentTwoBodyEnergy.cc
src/core/scoring/methods/ContextIndependentTwoBodyEnergy.fwd.hh
src/core/scoring/methods/ContextIndependentTwoBodyEnergy.hhShort ranged, context-independent, two-body energy class declaration
src/core/scoring/methods/CSD_TorsionEnergy.cc
src/core/scoring/methods/CSD_TorsionEnergy.fwd.hh
src/core/scoring/methods/CSD_TorsionEnergy.hh
src/core/scoring/methods/CustomAtomPairEnergy.ccSimple EnergyMethod for calculating residue-residue constraints under some interaction cutoff
src/core/scoring/methods/CustomAtomPairEnergy.fwd.hhStatistically derived rotamer pair potential class forward declaration
src/core/scoring/methods/CustomAtomPairEnergy.hh
src/core/scoring/methods/CustomAtomPairEnergyCreator.hhDeclaration for the class that connects CustomAtomPairEnergy with the ScoringManager
src/core/scoring/methods/DirectReadoutEnergy.ccStatistically derived DNA contact potential class implementation
src/core/scoring/methods/DirectReadoutEnergy.fwd.hh
src/core/scoring/methods/DirectReadoutEnergy.hhStatistically derived DNA contact potential class declaration
src/core/scoring/methods/DirectReadoutEnergyCreator.hhDeclaration for the class that connects DirectReadoutEnergy with the ScoringManager
src/core/scoring/methods/DistanceChainbreakEnergy.cc
src/core/scoring/methods/DistanceChainbreakEnergy.fwd.hh
src/core/scoring/methods/DistanceChainbreakEnergy.hh
src/core/scoring/methods/DistanceChainbreakEnergyCreator.hhDeclaration for the class that connects DistanceChainbreakEnergy with the ScoringManager
src/core/scoring/methods/DNA_BaseEnergy.cc
src/core/scoring/methods/DNA_BaseEnergy.fwd.hh
src/core/scoring/methods/DNA_BaseEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/DNA_BaseEnergyCreator.hhDeclaration for the class that connects DNA_BaseEnergy with the ScoringManager
src/core/scoring/methods/EnergyMethod.cc
src/core/scoring/methods/EnergyMethod.fwd.hhEnergy Method class forward declaration and EnergyMethodType enum definition
src/core/scoring/methods/EnergyMethod.hh
src/core/scoring/methods/EnergyMethodCreator.fwd.hhBase class for EnergyMethod factory-registration and creation classes
src/core/scoring/methods/EnergyMethodCreator.hhDeclaration of the base class for EnergyMethod factory registration and creation
src/core/scoring/methods/EnergyMethodOptions.cc
src/core/scoring/methods/EnergyMethodOptions.fwd.hh
src/core/scoring/methods/EnergyMethodOptions.hh
src/core/scoring/methods/EnergyMethodRegistrator.hhDeclaration of the base class for EnergyMethod factory registration and creation
src/core/scoring/methods/EnvEnergy.cc
src/core/scoring/methods/EnvEnergy.hhEnergyMethod that evaluates env and cbeta energies
src/core/scoring/methods/EnvEnergyCreator.hhDeclaration for the class that connects EnvEnergy with the ScoringManager
src/core/scoring/methods/EnvPairEnergy.fwd.hh
src/core/scoring/methods/EnvSmoothEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/EnvSmoothEnergy.fwd.hh
src/core/scoring/methods/EnvSmoothEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/EnvSmoothEnergyCreator.hhDeclaration for the class that connects EnvSmoothEnergy with the ScoringManager
src/core/scoring/methods/Fa_MbenvEnergy.cc
src/core/scoring/methods/Fa_MbenvEnergy.fwd.hhProbability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration
src/core/scoring/methods/Fa_MbenvEnergy.hh
src/core/scoring/methods/Fa_MbenvEnergyCreator.hhDeclaration for the class that connects Fa_MbenvEnergy with the ScoringManager
src/core/scoring/methods/Fa_MbsolvEnergy.cc
src/core/scoring/methods/Fa_MbsolvEnergy.fwd.hh
src/core/scoring/methods/Fa_MbsolvEnergy.hhLK Solvation using hemisphere culling class forward declaration
src/core/scoring/methods/Fa_MbsolvEnergyCreator.hhDeclaration for the class that connects Fa_MbsolvEnergy with the ScoringManager
src/core/scoring/methods/GaussianOverlapEnergy.ccGaussian Overlap Energy
src/core/scoring/methods/GaussianOverlapEnergy.fwd.hhGolap
src/core/scoring/methods/GaussianOverlapEnergy.hhEnergy of overlaps
src/core/scoring/methods/GaussianOverlapEnergyCreator.hhDeclaration for the class that connects GaussianOverlapEnergy with the ScoringManager
src/core/scoring/methods/GenBornEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/GenBornEnergy.fwd.hh
src/core/scoring/methods/GenBornEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/GenBornEnergyCreator.hhDeclaration for the class that connects GenBornEnergy with the ScoringManager
src/core/scoring/methods/HybridVDW_Energy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/HybridVDW_Energy.fwd.hh
src/core/scoring/methods/HybridVDW_Energy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/HybridVDW_EnergyCreator.hhDeclaration for the class that connects HybridVDW_Energy with the ScoringManager
src/core/scoring/methods/LinearChainbreakEnergy.cc
src/core/scoring/methods/LinearChainbreakEnergy.fwd.hh
src/core/scoring/methods/LinearChainbreakEnergy.hh
src/core/scoring/methods/LinearChainbreakEnergyCreator.ccLinearChainbreakEnergyCreator implementation
src/core/scoring/methods/LinearChainbreakEnergyCreator.hhDeclaration for the class that connects LinearChainbreakEnergy with the ScoringManager
src/core/scoring/methods/LK_BallEnergy.cc
src/core/scoring/methods/LK_BallEnergy.fwd.hh
src/core/scoring/methods/LK_BallEnergy.hhLK Solvation using hemisphere culling class declaration
src/core/scoring/methods/LK_BallEnergyCreator.hhDeclaration for the class that connects LK_BallEnergy with the ScoringManager
src/core/scoring/methods/LK_BallInfo.cc
src/core/scoring/methods/LK_BallInfo.hh
src/core/scoring/methods/LK_CosThetaEnergy.cc
src/core/scoring/methods/LK_CosThetaEnergy.fwd.hh
src/core/scoring/methods/LK_CosThetaEnergy.hhLK Solvation using hemisphere culling class forward declaration
src/core/scoring/methods/LK_CosThetaEnergyCreator.hhDeclaration for the class that connects LK_CosThetaEnergy with the ScoringManager
src/core/scoring/methods/LK_hack.cc
src/core/scoring/methods/LK_hack.fwd.hh
src/core/scoring/methods/LK_hack.hhLK Solvation using hemisphere culling class declaration
src/core/scoring/methods/LK_hackCreator.hhDeclaration for the class that connects LK_hack with the ScoringManager
src/core/scoring/methods/LongRangeTwoBodyEnergy.ccLong-Range, Two-Body Energy class implementation
src/core/scoring/methods/LongRangeTwoBodyEnergy.fwd.hhLong range two body energy method class forward declaration
src/core/scoring/methods/LongRangeTwoBodyEnergy.hhLong range two body energy method class declaration
src/core/scoring/methods/MembraneCbetaEnergy.cc
src/core/scoring/methods/MembraneCbetaEnergy.fwd.hh
src/core/scoring/methods/MembraneCbetaEnergy.hhMembrane Environment Cbeta Energy
src/core/scoring/methods/MembraneCbetaEnergyCreator.hhDeclaration for the class that connects MembraneCbetaEnergy with the ScoringManager
src/core/scoring/methods/MembraneCenPairEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/MembraneCenPairEnergy.fwd.hh
src/core/scoring/methods/MembraneCenPairEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/MembraneCenPairEnergyCreator.hhDeclaration for the class that connects MembraneCenPairEnergy with the ScoringManager
src/core/scoring/methods/MembraneEnvEnergy.cc
src/core/scoring/methods/MembraneEnvEnergy.fwd.hh
src/core/scoring/methods/MembraneEnvEnergy.hhMembrane Environment Cbeta Energy
src/core/scoring/methods/MembraneEnvEnergyCreator.hhDeclaration for the class that connects MembraneEnvEnergy with the ScoringManager
src/core/scoring/methods/MembraneEnvPenalties.cc
src/core/scoring/methods/MembraneEnvPenalties.fwd.hh
src/core/scoring/methods/MembraneEnvPenalties.hhRMS Energy function. Used to optimize the RMSD between two structures
src/core/scoring/methods/MembraneEnvPenaltiesCreator.hhDeclaration for the class that connects MembraneEnvPenalties with the ScoringManager
src/core/scoring/methods/MembraneEnvSmoothEnergy.ccStatistically derived smooth membrane environment potential class implementation
src/core/scoring/methods/MembraneEnvSmoothEnergy.fwd.hh
src/core/scoring/methods/MembraneEnvSmoothEnergy.hhStatistically derived smooth membrane environment potential class declaration
src/core/scoring/methods/MembraneEnvSmoothEnergyCreator.hhDeclaration for the class that connects MembraneEnvSmoothEnergy with the ScoringManager
src/core/scoring/methods/MembraneLipo.cc
src/core/scoring/methods/MembraneLipo.fwd.hh
src/core/scoring/methods/MembraneLipo.hhRMS Energy function. Used to optimize the RMSD between two structures
src/core/scoring/methods/MembraneLipoCreator.hhDeclaration for the class that connects MembraneLipo with the ScoringManager
src/core/scoring/methods/MetalloPlacementEnergy.ccLow-res placement score for metal sites
src/core/scoring/methods/MetalloPlacementEnergy.fwd.hh
src/core/scoring/methods/MetalloPlacementEnergy.hhLow-res placement score for metal sites
src/core/scoring/methods/Methods.hhEnergy Method enumeration
src/core/scoring/methods/MMBondAngleEnergy.cc
src/core/scoring/methods/MMBondAngleEnergy.fwd.hhMolecular mechanics bond angle energy forward declaration
src/core/scoring/methods/MMBondAngleEnergy.hhMolecular mechanics bond angle energy
src/core/scoring/methods/MMBondAngleEnergyCreator.hhDeclaration for the class that connects MMBondAngleEnergy with the ScoringManager
src/core/scoring/methods/MMBondLengthEnergy.cc
src/core/scoring/methods/MMBondLengthEnergy.fwd.hhMolecular mechanics bond length score class
src/core/scoring/methods/MMBondLengthEnergy.hhMolecular mechanics bond length score class
src/core/scoring/methods/MMBondLengthEnergyCreator.hhMolecular mechanics bond length score class
src/core/scoring/methods/MMLJEnergyInter.cc
src/core/scoring/methods/MMLJEnergyInter.fwd.hhMolecular mechanics lj energy forward declaration
src/core/scoring/methods/MMLJEnergyInter.hhMolecular mechanics lj energy
src/core/scoring/methods/MMLJEnergyInterCreator.hhDeclaration for the class that connects MMLJEnergyInter with the ScoringManager
src/core/scoring/methods/MMLJEnergyIntra.cc
src/core/scoring/methods/MMLJEnergyIntra.fwd.hhMolecular mechanics lj energy forward declaration
src/core/scoring/methods/MMLJEnergyIntra.hhMolecular mechanics lj energy
src/core/scoring/methods/MMLJEnergyIntraCreator.hhDeclaration for the class that connects MMLJEnergyIntra with the ScoringManager
src/core/scoring/methods/MMTorsionEnergy.cc
src/core/scoring/methods/MMTorsionEnergy.fwd.hhMolecular mechanics torsion energy forward declaration
src/core/scoring/methods/MMTorsionEnergy.hhMolecular mechanics torsion energy
src/core/scoring/methods/MMTorsionEnergyCreator.hhDeclaration for the class that connects MMTorsionEnergy with the ScoringManager
src/core/scoring/methods/OmegaTetherEnergy.ccOmegaTether energy method class implementation
src/core/scoring/methods/OmegaTetherEnergy.fwd.hhOmegaTether energy method class forward declaration
src/core/scoring/methods/OmegaTetherEnergy.hhOmegaTether energy method class declaration
src/core/scoring/methods/OmegaTetherEnergyCreator.hhDeclaration for the class that connects OmegaTetherEnergy with the ScoringManager
src/core/scoring/methods/OneBodyEnergy.cc
src/core/scoring/methods/OneBodyEnergy.fwd.hh
src/core/scoring/methods/OneBodyEnergy.hh
src/core/scoring/methods/P_AA_Energy.ccProbability of observing an amino acid (NOT conditional on phi/psi), energy method implementation
src/core/scoring/methods/P_AA_Energy.fwd.hhProbability of observing an amino acid (NOT conditional on phi/psi), energy method forward declaration
src/core/scoring/methods/P_AA_Energy.hhProbability of observing an amino acid (NOT conditional on phi/psi), energy method declaration
src/core/scoring/methods/P_AA_EnergyCreator.hhDeclaration for the class that connects P_AA_Energy with the ScoringManager
src/core/scoring/methods/P_AA_pp_Energy.cc
src/core/scoring/methods/P_AA_pp_Energy.fwd.hh
src/core/scoring/methods/P_AA_pp_Energy.hhProbability of observing an amino acid, given its phi/psi energy method declaration
src/core/scoring/methods/P_AA_pp_EnergyCreator.hhDeclaration for the class that connects P_AA_pp_Energy with the ScoringManager
src/core/scoring/methods/PackStatEnergy.ccRadius of gyration energy function definition. Returns -1 * RG for a given Pose
src/core/scoring/methods/PackStatEnergy.hh
src/core/scoring/methods/PackStatEnergyCreator.hhDeclaration for the class that connects PackStatEnergy with the ScoringManager
src/core/scoring/methods/PairEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/PairEnergy.fwd.hhStatistically derived rotamer pair potential class forward declaration
src/core/scoring/methods/PairEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/PairEnergyCreator.hhDeclaration for the class that connects PairEnergy with the ScoringManager
src/core/scoring/methods/PeptideBondEnergy.cc
src/core/scoring/methods/PeptideBondEnergy.fwd.hh
src/core/scoring/methods/PeptideBondEnergy.hhScoring method that defines ideal bond lengths between carbonyl carbon of residue N and nitrogen of residue N+1
src/core/scoring/methods/PeptideBondEnergyCreator.hhDeclaration for the class that connects PeptideBondEnergy with the ScoringManager
src/core/scoring/methods/pHEnergy.ccEnergy due to ionization state of the residue at a particular pH (see pHEnergy.hh for a detailed description)
src/core/scoring/methods/pHEnergy.fwd.hhPH energy forward declaration
src/core/scoring/methods/pHEnergy.hhPH Score (kT = 0.59 at 298 K) based on the chemical potential of the protonated/deprotonated residues. It indirectly contributes to a change in rotamer probabilities of protonated/deprotonated residues in the Dunbrack energy depending on the value of pH
src/core/scoring/methods/pHEnergyCreator.hhDeclaration for the class that connects pHEnergy with the ScoringManager
src/core/scoring/methods/PoissonBoltzmannEnergy.ccRamachandran energy method class implementation
src/core/scoring/methods/PoissonBoltzmannEnergy.fwd.hhRamachandran energy method class forward declaration
src/core/scoring/methods/PoissonBoltzmannEnergy.hhMembrane Environment Cbeta Energy
src/core/scoring/methods/PoissonBoltzmannEnergyCreator.hh
src/core/scoring/methods/ProClosureEnergy.ccProline ring closure energy method class implementation
src/core/scoring/methods/ProClosureEnergy.fwd.hhProline ring closure energy method class forward declaration
src/core/scoring/methods/ProClosureEnergy.hhProline ring closure energy method class declaration
src/core/scoring/methods/ProClosureEnergyCreator.hhDeclaration for the class that connects ProClosureEnergy with the ScoringManager
src/core/scoring/methods/PyEnergy.hhVarious Energy classes for subclassing in PyRosetta
src/core/scoring/methods/PyEnergyMethodRegisterer.hhEnergyMethod factory registration and creation in PyRosetta
src/core/scoring/methods/RamachandranEnergy.ccRamachandran energy method class implementation
src/core/scoring/methods/RamachandranEnergy.fwd.hhRamachandran energy method class forward declaration
src/core/scoring/methods/RamachandranEnergy.hhRamachandran energy method class declaration
src/core/scoring/methods/RamachandranEnergy2B.cc
src/core/scoring/methods/RamachandranEnergy2B.fwd.hh
src/core/scoring/methods/RamachandranEnergy2B.hhRamachandran energy method class declaration
src/core/scoring/methods/RamachandranEnergy2BCreator.hhDeclaration for the class that connects RamachandranEnergy2B with the ScoringManager
src/core/scoring/methods/RamachandranEnergyCreator.hhDeclaration for the class that connects RamachandranEnergy with the ScoringManager
src/core/scoring/methods/ReferenceEnergy.cc
src/core/scoring/methods/ReferenceEnergy.fwd.hhReference energy method forward declaration
src/core/scoring/methods/ReferenceEnergy.hhReference energy method implementation
src/core/scoring/methods/ReferenceEnergyCreator.hhDeclaration for the class that connects ReferenceEnergy with the ScoringManager
src/core/scoring/methods/ResidualDipolarCouplingEnergy.ccRDC energy - comparing experimental RDC values to calculated values
src/core/scoring/methods/ResidualDipolarCouplingEnergy.fwd.hh
src/core/scoring/methods/ResidualDipolarCouplingEnergy.hhRDC energy - comparing experimental RDC values to calculated values
src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.ccRDC energy - comparing experimental RDC values to calculated values
src/core/scoring/methods/ResidualDipolarCouplingEnergy_Rohl.hh
src/core/scoring/methods/ResidualDipolarCouplingEnergy_RohlCreator.hhDeclaration for the class that connects ResidualDipolarCouplingEnergy_Rohl with the ScoringManager
src/core/scoring/methods/ResidualDipolarCouplingEnergyCreator.hhDeclaration for the class that connects ResidualDipolarCouplingEnergy with the ScoringManager
src/core/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.ccRDC energy - comparing experimental RDC values to calculated values
src/core/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.fwd.hh
src/core/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.hhRDC energy - comparing experimental RDC values to calculated values
src/core/scoring/methods/RG_Energy.ccRadius of gyration energy function definition. Returns -1 * RG for a given Pose
src/core/scoring/methods/RG_Energy.hh
src/core/scoring/methods/RG_Energy_Fast.ccRadius of gyration energy function definition
src/core/scoring/methods/RG_Energy_Fast.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/RG_Energy_FastCreator.hhDeclaration for the class that connects RG_Energy_Fast with the ScoringManager
src/core/scoring/methods/RMS_Energy.ccRMS Energy function. Used to optimize the RMSD between two structures
src/core/scoring/methods/RMS_Energy.hhRMS Energy function. Used to optimize the RMSD between two structures
src/core/scoring/methods/RMS_EnergyCreator.hhDeclaration for the class that connects RMS_Energy with the ScoringManager
src/core/scoring/methods/SA_Energy.ccSa energy function definition
src/core/scoring/methods/SA_Energy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/SA_EnergyCreator.hh
src/core/scoring/methods/SecondaryStructureEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/SecondaryStructureEnergy.fwd.hh
src/core/scoring/methods/SecondaryStructureEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/SecondaryStructureEnergyCreator.hhDeclaration for the class that connects SecondaryStructureEnergy with the ScoringManager
src/core/scoring/methods/SequenceDependentRefEnergy.cc
src/core/scoring/methods/SequenceDependentRefEnergy.fwd.hhReference energy method forward declaration
src/core/scoring/methods/SequenceDependentRefEnergy.hhReference energy method implementation
src/core/scoring/methods/SequenceDependentRefEnergyCreator.hhDeclaration for the class that connects SequenceDependentRefEnergy with the ScoringManager
src/core/scoring/methods/ShortRangeTwoBodyEnergy.ccShort-Range, Two-Body Energy Method base class implementation
src/core/scoring/methods/ShortRangeTwoBodyEnergy.fwd.hhShort Range Two Body Energy Method base class forward declaration
src/core/scoring/methods/ShortRangeTwoBodyEnergy.hhShort Range Two Body Energy Method base class declaration
src/core/scoring/methods/SmoothCenPairEnergy.ccSmooth, differentiable, version of cenpair
src/core/scoring/methods/SmoothCenPairEnergy.hh
src/core/scoring/methods/SmoothCenPairEnergyCreator.hh
src/core/scoring/methods/SmoothEnvCenPairEnergy.fwd.hh
src/core/scoring/methods/SmoothEnvEnergy.ccSmooth, differentiable, version of centroid env
src/core/scoring/methods/SmoothEnvEnergy.hh
src/core/scoring/methods/SmoothEnvEnergyCreator.hh
src/core/scoring/methods/SuckerEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/SuckerEnergy.fwd.hhStatistically derived rotamer pair potential class forward declaration
src/core/scoring/methods/SuckerEnergy.hhEnergy attracting atoms to sucker atoms
src/core/scoring/methods/SuckerEnergyCreator.hhDeclaration for the class that connects SuckerEnergy with the ScoringManager
src/core/scoring/methods/SymmetricLigandEnergy.ccDunbrack energy method implementation
src/core/scoring/methods/SymmetricLigandEnergy.fwd.hhDunbrack energy method forward declaration
src/core/scoring/methods/SymmetricLigandEnergy.hhScore for implicit ligand interactions from symmetric geometry
src/core/scoring/methods/SymmetricLigandEnergyCreator.hh
src/core/scoring/methods/TwoBodyEnergy.ccTwo Body Energy Method base class implementation
src/core/scoring/methods/TwoBodyEnergy.fwd.hhTwo Body Energy Method base class forward declaration
src/core/scoring/methods/TwoBodyEnergy.hhTwo Body Energy Method base class declaration
src/core/scoring/methods/UnfoldedStateEnergy.ccUnfolded state energy method implementation; energies based on eneriges of residues in fragments
src/core/scoring/methods/UnfoldedStateEnergy.fwd.hhUnfolded state energy method, forward declaration
src/core/scoring/methods/UnfoldedStateEnergy.hhUnfolded state energy declaration header file
src/core/scoring/methods/UnfoldedStateEnergyCreator.hhDeclaration for the class that connects UnfoldedStateEnergy with the ScoringManager
src/core/scoring/methods/util.ccUtility methods for scoring
src/core/scoring/methods/util.hhUtility methods for scoring
src/core/scoring/methods/VDW_Energy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/methods/VDW_Energy.fwd.hh
src/core/scoring/methods/VDW_Energy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/methods/VDW_EnergyCreator.hhDeclaration for the class that connects VDW_Energy with the ScoringManager
src/core/scoring/methods/WaterAdductHBondEnergy.cc
src/core/scoring/methods/WaterAdductHBondEnergy.fwd.hh
src/core/scoring/methods/WaterAdductHBondEnergy.hhEnergy potential for water mediated hydrogen bonds involving adduct-placed water molecules
src/core/scoring/methods/WaterAdductHBondEnergyCreator.hhDeclaration for the class that connects WaterAdductHBondEnergy with the ScoringManager
src/core/scoring/methods/WaterAdductIntraEnergy.cc
src/core/scoring/methods/WaterAdductIntraEnergy.fwd.hh
src/core/scoring/methods/WaterAdductIntraEnergy.hhEnergetic offset/cost for placing a water adduct on an amino or nucleic acid
src/core/scoring/methods/WaterAdductIntraEnergyCreator.hhDeclaration for the class that connects WaterAdductIntraEnergy with the ScoringManager
src/core/scoring/methods/WholeStructureEnergy.ccImplementation of the EnergyMethod that applies to a whole structure and not on a residue-by-residue basis
src/core/scoring/methods/WholeStructureEnergy.fwd.hhEnergyMethod that applies to a whole structure and not on a residue-by-residue basis
src/core/scoring/methods/WholeStructureEnergy.hhEnergyMethod that applies to a whole structure and not on a residue-by-residue basis
src/core/scoring/methods/YHHPlanarityEnergy.cc
src/core/scoring/methods/YHHPlanarityEnergy.fwd.hh
src/core/scoring/methods/YHHPlanarityEnergy.hhTerm for chi3 on tyrosine residues to prefer the hydrogen lie in the plane of the ring
src/core/scoring/methods/YHHPlanarityEnergyCreator.hh
src/core/scoring/methods/dfire/DFIRE_Energy.cc
src/core/scoring/methods/dfire/DFIRE_Energy.fwd.hh
src/core/scoring/methods/dfire/DFIRE_Energy.hh
src/core/scoring/methods/dfire/DFIRE_EnergyCreator.hh
src/core/scoring/methods/dfire/DFIRE_Potential.cc
src/core/scoring/methods/dfire/DFIRE_Potential.fwd.hh
src/core/scoring/methods/dfire/DFIRE_Potential.hhDFIRE Potential class declaration
src/core/scoring/mm/MMBondAngleLibrary.cc
src/core/scoring/mm/MMBondAngleLibrary.fwd.hhCore::scoring::mm::MMBondAngleLibrary forward declarations
src/core/scoring/mm/MMBondAngleLibrary.hhMolecular mechanics bond angle library class
src/core/scoring/mm/MMBondAngleResidueTypeParam.ccClass to store bond angle parameters for a particular ResidueType
src/core/scoring/mm/MMBondAngleResidueTypeParam.fwd.hhCore::scoring::mm::MMBondAngleResidueTypeParam forward declarations
src/core/scoring/mm/MMBondAngleResidueTypeParam.hhClass to store bond angle parameters for a particular ResidueType
src/core/scoring/mm/MMBondAngleResidueTypeParamSet.cc
src/core/scoring/mm/MMBondAngleResidueTypeParamSet.fwd.hhCore::scoring::mm::MMBondAngleResidueTypeParamSet forward declarations
src/core/scoring/mm/MMBondAngleResidueTypeParamSet.hhClass to store bond angle parameters for a set of ResidueTypes
src/core/scoring/mm/MMBondAngleScore.ccMolecular mechanics bond angle score class
src/core/scoring/mm/MMBondAngleScore.fwd.hhCore::scoring::mm::MMBondAngleScore forward declarations
src/core/scoring/mm/MMBondAngleScore.hhMolecular mechanics bond angle score class
src/core/scoring/mm/MMBondLengthLibrary.cc
src/core/scoring/mm/MMBondLengthLibrary.fwd.hhMolecular mechanics bond length score class
src/core/scoring/mm/MMBondLengthLibrary.hhMolecular mechanics bond length score class
src/core/scoring/mm/MMBondLengthScore.ccMolecular mechanics bond length score class
src/core/scoring/mm/MMBondLengthScore.fwd.hhMolecular mechanics bond length score class
src/core/scoring/mm/MMBondLengthScore.hhMolecular mechanics bond length score class
src/core/scoring/mm/MMLJEnergyTable.ccMolecular mechanics lj energy table class
src/core/scoring/mm/MMLJEnergyTable.fwd.hhCore::scoring::mm::MMLJEnergyTable forward declarations
src/core/scoring/mm/MMLJEnergyTable.hhMolecular mechanics lj score class
src/core/scoring/mm/MMLJLibrary.cc
src/core/scoring/mm/MMLJLibrary.fwd.hhCore::scoring::mm::MMLJLibrary forward declarations
src/core/scoring/mm/MMLJLibrary.hhMolecular mechanics lj library class
src/core/scoring/mm/MMLJScore.ccMolecular mechanics lj score class
src/core/scoring/mm/MMLJScore.fwd.hhCore::scoring::mm::MMLJScore forward declarations
src/core/scoring/mm/MMLJScore.hhMolecular mechanics lj score class
src/core/scoring/mm/MMTorsionLibrary.cc
src/core/scoring/mm/MMTorsionLibrary.fwd.hhCore::scoring::mm::MMTorsionLibrary forward declarations
src/core/scoring/mm/MMTorsionLibrary.hhMolecular mechanics torsion library class
src/core/scoring/mm/MMTorsionScore.ccMolecular mechanics torsion score class
src/core/scoring/mm/MMTorsionScore.fwd.hhCore::scoring::mm::MMTorsionScore forward declarations
src/core/scoring/mm/MMTorsionScore.hhMolecular mechanics torsion score class
src/core/scoring/mm/mmtrie/MMEnergyTableAtom.ccImplimentation for the MMEnergyTableAtom. Heavily coppied from the EtableAtom.cc
src/core/scoring/mm/mmtrie/MMEnergyTableAtom.fwd.hhForward header for the MMEnergyTableAtom. Heavily coppied from the EtableAtom.fwd.hh
src/core/scoring/mm/mmtrie/MMEnergyTableAtom.hhHeader for the MMEnergyTableAtom. Heavily coppied from the EtableAtom.hh
src/core/scoring/mm/mmtrie/MMEnergyTableRotamerTrie.fwd.hh
src/core/scoring/nv/NVlookup.cc
src/core/scoring/nv/NVlookup.fwd.hh
src/core/scoring/nv/NVlookup.hh
src/core/scoring/nv/NVscore.cc
src/core/scoring/nv/NVscore.fwd.hh
src/core/scoring/nv/NVscore.hh
src/core/scoring/nv/NVscoreCreator.hh
src/core/scoring/orbitals/OrbitalsAssigned.cc
src/core/scoring/orbitals/OrbitalsAssigned.hh
src/core/scoring/orbitals/OrbitalsLookup.cc
src/core/scoring/orbitals/OrbitalsLookup.fwd.hh
src/core/scoring/orbitals/OrbitalsLookup.hh
src/core/scoring/orbitals/OrbitalsScore.cc
src/core/scoring/orbitals/OrbitalsScore.fwd.hh
src/core/scoring/orbitals/OrbitalsScore.hh
src/core/scoring/orbitals/OrbitalsScoreCreator.hh
src/core/scoring/orbitals/OrbitalsStatistics.cc
src/core/scoring/orbitals/OrbitalsStatistics.hh
src/core/scoring/orbitals/OrbitalStatistics.fwd.hh
src/core/scoring/packing/Ball.hh
src/core/scoring/packing/compute_holes_score.ccPacking Score
src/core/scoring/packing/compute_holes_score.hhPacking Score
src/core/scoring/packing/compute_holes_score_res.ccPacking Score
src/core/scoring/packing/compute_holes_score_res.hhPacking Score
src/core/scoring/packing/HolesEnergy.cc
src/core/scoring/packing/HolesEnergy.hhPacking Score
src/core/scoring/packing/HolesEnergyCreator.hhDeclaration for the class that connects HolesEnergy with the ScoringManager
src/core/scoring/packing/HolesEnergyRes.cc
src/core/scoring/packing/HolesEnergyRes.hhPacking Score
src/core/scoring/packing/HolesParams.hh
src/core/scoring/packing/HolesParamsRes.hh
src/core/scoring/packing/PoseBalls.cc
src/core/scoring/packing/PoseBalls.hh
src/core/scoring/packing/PoseBallsLite.cc
src/core/scoring/packing/PoseBallsLite.hh
src/core/scoring/packing/surf_vol.ccPacking Score
src/core/scoring/packing/surf_vol.hh
src/core/scoring/packing/SurfEnergy.ccPacking Score
src/core/scoring/packing/SurfEnergy.hhPacking Score
src/core/scoring/packing/SurfEnergyCreator.hhDeclaration for the class that connects SurfEnergy with the ScoringManager
src/core/scoring/packing/SurfVolEnergy.ccPacking Score
src/core/scoring/packing/SurfVolEnergy.hhPacking Score
src/core/scoring/packing/SurfVolEnergyCreator.hhDeclaration for the class that connects SurfVolEnergy with the ScoringManager
src/core/scoring/packstat/AtomRadiusMap.cc
src/core/scoring/packstat/AtomRadiusMap.fwd.hh
src/core/scoring/packstat/AtomRadiusMap.hh
src/core/scoring/packstat/CavityBall.cc
src/core/scoring/packstat/CavityBall.fwd.hh
src/core/scoring/packstat/CavityBall.hh
src/core/scoring/packstat/compute_sasa.cc
src/core/scoring/packstat/compute_sasa.hh
src/core/scoring/packstat/io.cc
src/core/scoring/packstat/io.hh
src/core/scoring/packstat/LeeRichards.cc
src/core/scoring/packstat/LeeRichards.hh
src/core/scoring/packstat/packing_score_params.cc
src/core/scoring/packstat/packing_score_params.hh
src/core/scoring/packstat/PackingScore.cc
src/core/scoring/packstat/PackingScore.hh
src/core/scoring/packstat/sasa_dot_locations.hh
src/core/scoring/packstat/SimplePDB.cc
src/core/scoring/packstat/SimplePDB.fwd.hh
src/core/scoring/packstat/SimplePDB.hh
src/core/scoring/packstat/SimplePDB_Atom.cc
src/core/scoring/packstat/SimplePDB_Atom.fwd.hh
src/core/scoring/packstat/SimplePDB_Atom.hh
src/core/scoring/packstat/types.hh
src/core/scoring/packstat/util.hh
src/core/scoring/rna/RG_Energy_RNA.cc
src/core/scoring/rna/RG_Energy_RNA.hh
src/core/scoring/rna/RG_Energy_RNACreator.hhDeclaration for the class that connects RG_Energy_RNA with the ScoringManager
src/core/scoring/rna/RNA_AtomVDW.cc
src/core/scoring/rna/RNA_AtomVDW.fwd.hh
src/core/scoring/rna/RNA_AtomVDW.hh
src/core/scoring/rna/RNA_BaseBaseEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/rna/RNA_BaseBaseEnergy.fwd.hh
src/core/scoring/rna/RNA_BaseBaseEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/rna/RNA_BaseDoubletClasses.hh
src/core/scoring/rna/RNA_BulgeEnergy.cc
src/core/scoring/rna/RNA_BulgeEnergy.fwd.hh
src/core/scoring/rna/RNA_BulgeEnergy.hhScore function class
src/core/scoring/rna/RNA_BulgeEnergyCreator.hh
src/core/scoring/rna/RNA_CentroidInfo.cc
src/core/scoring/rna/RNA_CentroidInfo.fwd.hh
src/core/scoring/rna/RNA_CentroidInfo.hh
src/core/scoring/rna/RNA_DataBackboneEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/rna/RNA_DataBackboneEnergy.fwd.hh
src/core/scoring/rna/RNA_DataBackboneEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/rna/RNA_DataBackboneEnergyCreator.hhDeclaration for the class that connects RNA_DataBackboneEnergy with the ScoringManager
src/core/scoring/rna/RNA_DataInfo.cc
src/core/scoring/rna/RNA_DataInfo.fwd.hh
src/core/scoring/rna/RNA_DataInfo.hh
src/core/scoring/rna/RNA_FA_Stack.hh
src/core/scoring/rna/RNA_FilteredBaseBaseInfo.cc
src/core/scoring/rna/RNA_FilteredBaseBaseInfo.fwd.hh
src/core/scoring/rna/RNA_FilteredBaseBaseInfo.hh
src/core/scoring/rna/RNA_FittedTorsionInfo.ccStatistically derived torsion information for RNA
src/core/scoring/rna/RNA_FittedTorsionInfo.hhStatistically derived torsion information for RNA
src/core/scoring/rna/RNA_FullAtomStackingEnergy.cc
src/core/scoring/rna/RNA_FullAtomStackingEnergy.fwd.hh
src/core/scoring/rna/RNA_FullAtomStackingEnergy.hh
src/core/scoring/rna/RNA_FullAtomStackingEnergyCreator.hhDeclaration for the class that connects RNA_FullAtomStackingEnergy with the ScoringManager
src/core/scoring/rna/RNA_FullAtomVDW_BasePhosphate.cc
src/core/scoring/rna/RNA_FullAtomVDW_BasePhosphate.fwd.hh
src/core/scoring/rna/RNA_FullAtomVDW_BasePhosphate.hhFullAtom VDW energy between the base and phosphate group in the same (intra) nucleotide
src/core/scoring/rna/RNA_FullAtomVDW_BasePhosphateCreator.fwd.hh
src/core/scoring/rna/RNA_FullAtomVDW_BasePhosphateCreator.hh
src/core/scoring/rna/RNA_LJ_BaseEnergy.cc
src/core/scoring/rna/RNA_LJ_BaseEnergy.fwd.hh
src/core/scoring/rna/RNA_LJ_BaseEnergy.hhVan der waals over aromatics
src/core/scoring/rna/RNA_LJ_BaseEnergyCreator.hhDeclaration for the class that connects RNA_LJ_BaseEnergy with the ScoringManager
src/core/scoring/rna/RNA_LowResolutionPotential.cc
src/core/scoring/rna/RNA_LowResolutionPotential.fwd.hh
src/core/scoring/rna/RNA_LowResolutionPotential.hh
src/core/scoring/rna/RNA_PairwiseLowResolutionEnergy.ccStatistically derived rotamer pair potential class implementation
src/core/scoring/rna/RNA_PairwiseLowResolutionEnergy.fwd.hh
src/core/scoring/rna/RNA_PairwiseLowResolutionEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/rna/RNA_PairwiseLowResolutionEnergyCreator.hhDeclaration for the class that connects RNA_PairwiseLowResolutionEnergy with the ScoringManager
src/core/scoring/rna/RNA_RawBaseBaseInfo.cc
src/core/scoring/rna/RNA_RawBaseBaseInfo.fwd.hh
src/core/scoring/rna/RNA_RawBaseBaseInfo.hh
src/core/scoring/rna/RNA_ScoringInfo.cc
src/core/scoring/rna/RNA_ScoringInfo.fwd.hh
src/core/scoring/rna/RNA_ScoringInfo.hh
src/core/scoring/rna/RNA_SugarCloseEnergy.cc
src/core/scoring/rna/RNA_SugarCloseEnergy.fwd.hh
src/core/scoring/rna/RNA_SugarCloseEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/rna/RNA_SugarCloseEnergyCreator.hh
src/core/scoring/rna/RNA_Torsion.fwd.hh
src/core/scoring/rna/RNA_TorsionEnergy.cc
src/core/scoring/rna/RNA_TorsionEnergy.fwd.hh
src/core/scoring/rna/RNA_TorsionEnergy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/rna/RNA_TorsionEnergyCreator.hhDeclaration for the class that connects RNA_TorsionEnergy with the ScoringManager
src/core/scoring/rna/RNA_TorsionPotential.cc
src/core/scoring/rna/RNA_TorsionPotential.fwd.hh
src/core/scoring/rna/RNA_TorsionPotential.hh
src/core/scoring/rna/RNA_Util.cc
src/core/scoring/rna/RNA_Util.hh
src/core/scoring/rna/RNA_VDW_Energy.cc
src/core/scoring/rna/RNA_VDW_Energy.fwd.hh
src/core/scoring/rna/RNA_VDW_Energy.hhStatistically derived rotamer pair potential class declaration
src/core/scoring/rna/RNA_VDW_EnergyCreator.hhDeclaration for the class that connects RNA_VDW_Energy with the ScoringManager
src/core/scoring/saxs/DistanceHistogram.fwd.hhForward declaration of a DistanceHistogram data type
src/core/scoring/saxs/DistanceHistogram.hh
src/core/scoring/saxs/FastSAXSEnergy.cc
src/core/scoring/saxs/FastSAXSEnergy.hh
src/core/scoring/saxs/FastSAXSEnergyCreator.hhEnergy Creator for FastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
src/core/scoring/saxs/FormFactor.ccRepresents an atomic scattering form factor
src/core/scoring/saxs/FormFactor.fwd.hhForward declaration of a form factor data type
src/core/scoring/saxs/FormFactor.hhCollects histogram of distances between atoms of given SAXS-types, e.g. distances between ARG-CEN and TRP-CEN
src/core/scoring/saxs/FormFactorManager.ccLoads and manages atomic form factors
src/core/scoring/saxs/FormFactorManager.fwd.hhForward declaration of a form factor manager
src/core/scoring/saxs/FormFactorManager.hhLoads and manages atomic form factors
src/core/scoring/saxs/SAXSEnergy.ccFastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
src/core/scoring/saxs/SAXSEnergy.hhFastSAX scoring of Stovgaard et al (BMC Bioinf. 2010)
src/core/scoring/saxs/SAXSEnergyCEN.hh
src/core/scoring/saxs/SAXSEnergyCreator.hhDeclaration for the class that connects SAXSEnergyCreator with the ScoringManager
src/core/scoring/saxs/SAXSEnergyCreatorCEN.cc
src/core/scoring/saxs/SAXSEnergyCreatorCEN.hhDeclaration for the class that connects SAXSEnergyCreatorCEN with the ScoringManager
src/core/scoring/saxs/SAXSEnergyCreatorFA.cc
src/core/scoring/saxs/SAXSEnergyCreatorFA.hhDeclaration for the class that connects SAXSEnergyCreatorFA with the ScoringManager
src/core/scoring/saxs/SAXSEnergyFA.hh
src/core/scoring/saxs/SinXOverX.cc
src/core/scoring/saxs/SinXOverX.hh
src/core/scoring/sc/ShapeComplementarityCalculator.cc
src/core/scoring/sc/ShapeComplementarityCalculator.fwd.hhHeaders for the Shape Complementarity Calculator
src/core/scoring/sc/ShapeComplementarityCalculator.hhHeaders for the Shape Complementarity Calculator
src/core/scoring/sc/ShapeComplementarityCalculator_Private.hh
src/core/scoring/solid_surface/SurfaceEnergies.ccSurfaceEnergies class avoids calculating energies between surface residues, and detecting their neighbor relationships
src/core/scoring/solid_surface/SurfaceEnergies.fwd.hhSurfaceEnergies forward declarations header
src/core/scoring/solid_surface/SurfaceEnergies.hhSurfaceEnergies class
src/core/scoring/sym_e/symE.cc
src/core/scoring/sym_e/symE.fwd.hh
src/core/scoring/sym_e/symE.hh
src/core/scoring/sym_e/symECreator.hh
src/core/scoring/symmetry/NBListCache.fwd.hh
src/core/scoring/symmetry/NBListCache.hh
src/core/scoring/symmetry/SymmetricEnergies.cc
src/core/scoring/symmetry/SymmetricEnergies.fwd.hhSymmetric Energies class to store cached energies and track the residue neighbor relationships
src/core/scoring/symmetry/SymmetricEnergies.hhSymmetric Energies class to store cached energies and track the residue neighbor relationships
src/core/scoring/symmetry/SymmetricScoreFunction.cc
src/core/scoring/symmetry/SymmetricScoreFunction.fwd.hhCore::scoring::symmetry::SymmetricScoreFunction forward declarations
src/core/scoring/symmetry/SymmetricScoreFunction.hhSymmetric Score function class
src/core/scoring/trie/CPDataCorrespondence.cc
src/core/scoring/trie/CPDataCorrespondence.fwd.hh
src/core/scoring/trie/CPDataCorrespondence.hh
src/core/scoring/trie/RotamerDescriptor.fwd.hh
src/core/scoring/trie/RotamerDescriptor.hh
src/core/scoring/trie/RotamerTrie.fwd.hh
src/core/scoring/trie/RotamerTrie.hh
src/core/scoring/trie/RotamerTrieBase.fwd.hh
src/core/scoring/trie/RotamerTrieBase.hh
src/core/scoring/trie/trie.functions.fwd.hh
src/core/scoring/trie/trie.functions.hh
src/core/scoring/trie/trie_vs_path.cc
src/core/scoring/trie/trie_vs_path.hh
src/core/scoring/trie/trie_vs_trie.cc
src/core/scoring/trie/trie_vs_trie.fwd.hh
src/core/scoring/trie/trie_vs_trie.hh
src/core/scoring/trie/TrieCollection.cc
src/core/scoring/trie/TrieCollection.fwd.hh
src/core/scoring/trie/TrieCollection.hhContainer class for storing rotamer tries in an Energies object
src/core/scoring/trie/TrieCountPairBase.cc
src/core/scoring/trie/TrieCountPairBase.fwd.hh
src/core/scoring/trie/TrieCountPairBase.hh
src/core/sequence/Aligner.ccClass definition for a class that aligns two Sequence objects using dynamic programming algorithms
src/core/sequence/Aligner.fwd.hhForward declaration for Aligner class
src/core/sequence/Aligner.hhClass definition for a class that aligns two Sequence objects using an dynamic programming and an arbitrary scoring scheme
src/core/sequence/AlignerFactory.cc
src/core/sequence/AlignerFactory.hh
src/core/sequence/AnnotatedSequence.cc
src/core/sequence/AnnotatedSequence.hh
src/core/sequence/BasicSequenceCreators.cc
src/core/sequence/BasicSequenceCreators.hh
src/core/sequence/CacheableSequenceProfile.fwd.hh
src/core/sequence/CacheableSequenceProfile.hh
src/core/sequence/ChemicalShiftScoringScheme.ccMethod implementations for ChemicalShiftScoringScheme class
src/core/sequence/ChemicalShiftScoringScheme.hh
src/core/sequence/ChemicalShiftSequence.cc
src/core/sequence/ChemicalShiftSequence.fwd.hhForward declaration for class ChemicalShiftSequence
src/core/sequence/ChemicalShiftSequence.hhClass definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position
src/core/sequence/CompassScoringScheme.ccMethod implementations for CompassScoringScheme class
src/core/sequence/CompassScoringScheme.hhClass definition for a profile-profile scoring scheme for comparing two sequence profiles using the Compass method, published by Sadreyev and Grishin
src/core/sequence/CompositeScoringScheme.ccClass definition for a given scoring scheme for an alignment
src/core/sequence/CompositeScoringScheme.fwd.hhForward declaration for CompositeScoringScheme.fwd.hh
src/core/sequence/CompositeScoringScheme.hhClass definition for a given scoring scheme for an alignment
src/core/sequence/CompositeSequence.cc
src/core/sequence/CompositeSequence.fwd.hhForward declaration for class CompositeSequence
src/core/sequence/CompositeSequence.hhClass definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position
src/core/sequence/DerivedSequenceMapping.cc
src/core/sequence/DerivedSequenceMapping.fwd.hh
src/core/sequence/DerivedSequenceMapping.hh
src/core/sequence/DP_Matrix.cc
src/core/sequence/DP_Matrix.hhClass for holding information on a dynamic programming matrix
src/core/sequence/DPScoringScheme.ccMethod implementations for DPScoringScheme class
src/core/sequence/DPScoringScheme.hhClass definition for a profile-profile scoring scheme for comparing two sequence profiles using the DP city-block distance
src/core/sequence/ExtendAlignerSW.cc
src/core/sequence/ExtendAlignerSW.hhClass definition for a class that aligns two takes a seed sequence alignment and extends it using the Smith-Waterman alignment algorithm
src/core/sequence/L1ScoringScheme.ccMethod implementations for L1ScoringScheme class
src/core/sequence/L1ScoringScheme.hhClass definition for a profile-profile scoring scheme for comparing two sequence profiles using the L1 city-block distance
src/core/sequence/MatrixScoringScheme.ccClass definition for a given scoring scheme for an alignment
src/core/sequence/MatrixScoringScheme.hhClass definition for a given scoring scheme for an alignment
src/core/sequence/MCAligner.ccClass definition for a class that aligns two Sequence objects using a stochastic version of the Needleman-Wunsch algorithm
src/core/sequence/MCAligner.hhClass definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm
src/core/sequence/NWAligner.ccClass definition for a class that aligns two Sequence objects using the Needleman-Wunsch alignment algorithm
src/core/sequence/NWAligner.fwd.hhForward declaration for NWAligner class
src/core/sequence/NWAligner.hhClass definition for a class that aligns two Sequence objects using a the Needleman-Wunsch alignment algorithm
src/core/sequence/PairScoringScheme.cc
src/core/sequence/PairScoringScheme.fwd.hhForward declaration for PairScoringScheme.fwd.hh
src/core/sequence/PairScoringScheme.hhClass definition for a given scoring scheme for an alignment
src/core/sequence/ProfSimScoringScheme.cc
src/core/sequence/ProfSimScoringScheme.hhClass definition for a given scoring scheme for an alignment
src/core/sequence/ScoringScheme.ccAbstract base class for representing scoring schemes for alignments
src/core/sequence/ScoringScheme.fwd.hhForward declaration for ScoringScheme.fwd.hh
src/core/sequence/ScoringScheme.hh
src/core/sequence/ScoringSchemeFactory.ccFactory for creating various types of ScoringSchemes for use in sequence alignment
src/core/sequence/ScoringSchemeFactory.hh
src/core/sequence/Sequence.ccMethod definitions for Sequence class
src/core/sequence/Sequence.fwd.hhForward declaration for Sequence class
src/core/sequence/Sequence.hhClass definition for a sequence
src/core/sequence/SequenceAlignment.cc
src/core/sequence/SequenceAlignment.fwd.hhForward declaration for SequenceAlignment class
src/core/sequence/SequenceAlignment.hhClass definition for a multiple sequence alignment
src/core/sequence/SequenceCoupling.cc
src/core/sequence/SequenceCoupling.fwd.hh
src/core/sequence/SequenceCoupling.hhClass definition for a sequence coupling profile that
src/core/sequence/SequenceCreator.cc
src/core/sequence/SequenceCreator.fwd.hh
src/core/sequence/SequenceCreator.hhBase class for SequenceCreators for the Sequence load-time factory registration scheme
src/core/sequence/SequenceFactory.ccFactory for creating various types of sequences
src/core/sequence/SequenceFactory.fwd.hh
src/core/sequence/SequenceFactory.hhFactory for creating various types of sequence
src/core/sequence/SequenceProfile.ccClass definition for a given scoring scheme for an alignment
src/core/sequence/SequenceProfile.fwd.hhForward declaration for class SequenceProfile
src/core/sequence/SequenceProfile.hhClass definition for a sequence profile that represents each position in a sequence as a probability distribution over the allowed amino acids at that position
src/core/sequence/SimpleScoringScheme.ccClass definition for a given scoring scheme for an alignment
src/core/sequence/SimpleScoringScheme.hhClass definition for a given scoring scheme for an alignment
src/core/sequence/SWAligner.cc
src/core/sequence/SWAligner.fwd.hhForward declaration for SWAligner class
src/core/sequence/SWAligner.hhClass definition for a class that aligns two Sequence objects using ScoringScheme and the Smith-Waterman alignment algorithm
src/core/sequence/util.ccSmall bundle of utilities for dealing with sequences
src/core/sequence/util.hh
src/core/util/ABEGOManager.ccClass for ABEGO
src/core/util/ABEGOManager.fwd.hhFoward header file for class of ABEGO
src/core/util/ABEGOManager.hhHeader file for class of ABEGO plus
src/core/util/ChainbreakUtil.cc
src/core/util/ChainbreakUtil.hh
src/core/util/disulfide_util.ccA collection of procedures for manipulating disulfide bonds
src/core/util/disulfide_util.hhA collection of procedures for manipulating disulfide bonds
src/core/util/kinematics_util.cc
src/core/util/kinematics_util.hh
src/core/util/SwitchResidueTypeSet.ccFunctions for switching the residue type set of a pose
src/core/util/SwitchResidueTypeSet.hhFunctions for switching the residue type set of a pose
src/protocols/abinitio/AbrelaxApplication.cc
src/protocols/abinitio/AbrelaxApplication.hh
src/protocols/abinitio/AbrelaxMover.ccThis class will be handled to a SampleProtocol as a control instance
src/protocols/abinitio/AbrelaxMover.fwd.hh
src/protocols/abinitio/AbrelaxMover.hh
src/protocols/abinitio/AllResiduesChanged.hh
src/protocols/abinitio/BrokerMain.cc
src/protocols/abinitio/BrokerMain.hh
src/protocols/abinitio/ClassicAbinitio.ccAb-initio fragment assembly protocol for proteins
src/protocols/abinitio/ClassicAbinitio.fwd.hh
src/protocols/abinitio/ClassicAbinitio.hhHeader file for ClassicAbinitio protocol
src/protocols/abinitio/ConstraintFragmentSampler.ccAb-initio fragment assembly protocol for proteins
src/protocols/abinitio/ConstraintFragmentSampler.hhHeader file for ConstraintFragmentSampler protocol
src/protocols/abinitio/DomainAssembly.cc
src/protocols/abinitio/DomainAssembly.hh
src/protocols/abinitio/DomainAssemblyCreator.hhDeclaration of the MoverCreator class for the DomainAssembly
src/protocols/abinitio/DoubleLayerKinematicAbinitio.cc
src/protocols/abinitio/DoubleLayerKinematicAbinitio.fwd.hh
src/protocols/abinitio/DoubleLayerKinematicAbinitio.hh
src/protocols/abinitio/FoldConstraints.ccAb-initio fragment assembly protocol for proteins under the influence of contraints (e.g., NOE)
src/protocols/abinitio/FoldConstraints.fwd.hh
src/protocols/abinitio/FoldConstraints.hhAbinitio-Folding under (distance-)constraints
src/protocols/abinitio/FragmentCost.hh
src/protocols/abinitio/FragmentSampler.ccAb-initio fragment assembly protocol for proteins
src/protocols/abinitio/FragmentSampler.fwd.hh
src/protocols/abinitio/FragmentSampler.hhHeader file for FragmentSampler protocol
src/protocols/abinitio/IterativeAbrelax.cc
src/protocols/abinitio/IterativeAbrelax.hh
src/protocols/abinitio/IterativeBase.cc
src/protocols/abinitio/IterativeBase.hh
src/protocols/abinitio/IterativeCentroid.cc
src/protocols/abinitio/IterativeCentroid.hh
src/protocols/abinitio/IterativeFullatom.cc
src/protocols/abinitio/IterativeFullatom.hh
src/protocols/abinitio/JumpingFoldConstraints.hh
src/protocols/abinitio/KinematicAbinitio.cc
src/protocols/abinitio/KinematicAbinitio.fwd.hh
src/protocols/abinitio/KinematicAbinitio.hhAbinitio - Type sampling controlled by KinematicControl object
src/protocols/abinitio/KinematicControl.cc
src/protocols/abinitio/KinematicControl.fwd.hh
src/protocols/abinitio/KinematicControl.hh
src/protocols/abinitio/KinematicTaskControl.cc
src/protocols/abinitio/KinematicTaskControl.fwd.hh
src/protocols/abinitio/KinematicTaskControl.hh
src/protocols/abinitio/LoopJumpFoldCst.cc
src/protocols/abinitio/LoopJumpFoldCst.fwd.hh
src/protocols/abinitio/LoopJumpFoldCst.hh
src/protocols/abinitio/MembraneAbinitio.ccAb-initio fragment assembly protocol for membrane proteins
src/protocols/abinitio/MembraneAbinitio.fwd.hh
src/protocols/abinitio/MembraneAbinitio.hhHeader file for MembraneAbinitio protocol
src/protocols/abinitio/PairingStatistics.cc
src/protocols/abinitio/PairingStatistics.fwd.hh
src/protocols/abinitio/PairingStatistics.hh
src/protocols/abinitio/Protocol.cc
src/protocols/abinitio/Protocol.fwd.hh
src/protocols/abinitio/Protocol.hh
src/protocols/abinitio/ResolutionSwitcher.cc
src/protocols/abinitio/ResolutionSwitcher.fwd.hh
src/protocols/abinitio/ResolutionSwitcher.hh
src/protocols/abinitio/StrandConstraints.cc
src/protocols/abinitio/StrandConstraints.hh
src/protocols/abinitio/Template.cc
src/protocols/abinitio/Template.fwd.hh
src/protocols/abinitio/Template.hh
src/protocols/abinitio/TemplateJumpSetup.cc
src/protocols/abinitio/TemplateJumpSetup.fwd.hh
src/protocols/abinitio/TemplateJumpSetup.hh
src/protocols/abinitio/Templates.cc
src/protocols/abinitio/Templates.fwd.hh
src/protocols/abinitio/Templates.hh
src/protocols/abinitio/vs_test.cc
src/protocols/abinitio/vs_test.hh
src/protocols/analysis/InterfaceAnalyzerMover.ccInterfaceAnalyzerMover implementation - class for in-depth interface quality analysis
src/protocols/analysis/InterfaceAnalyzerMover.fwd.hhFwd declaration for InterfaceAnalyzer: intense analysis of interface quality
src/protocols/analysis/InterfaceAnalyzerMover.hh
src/protocols/analysis/InterfaceAnalyzerMoverCreator.hhThis class will create instances of Mover InterfaceAnalyzerMover for the MoverFactory
src/protocols/analysis/LoopAnalyzerMover.ccLoopAnalyzerMover implementation - class for in-depth loop structure quality analysis
src/protocols/analysis/LoopAnalyzerMover.fwd.hhFwd declaration for LoopAnalyzer: intense analysis of loop quality
src/protocols/analysis/LoopAnalyzerMover.hhLoopAnalyzerMover examines loop structures and packages extra scores into a Job object
src/protocols/analysis/PackStatMover.cc
src/protocols/analysis/PackStatMover.fwd.hh
src/protocols/analysis/PackStatMover.hh
src/protocols/anchored_design/Anchor.cc
src/protocols/anchored_design/Anchor.fwd.hh
src/protocols/anchored_design/Anchor.hh
src/protocols/anchored_design/AnchorMovers.cc
src/protocols/anchored_design/AnchorMovers.fwd.hh
src/protocols/anchored_design/AnchorMovers.hh
src/protocols/anchored_design/AnchorMoversData.cc
src/protocols/anchored_design/AnchorMoversData.fwd.hh
src/protocols/anchored_design/AnchorMoversData.hh
src/protocols/antibody/AntibodyClass.cc
src/protocols/antibody/AntibodyClass.fwd.hhAntibody class forward declarations header
src/protocols/antibody/AntibodyClass.hh
src/protocols/antibody/AntibodyModeler.cc
src/protocols/antibody/AntibodyModeler.fwd.hhForward declaration
src/protocols/antibody/AntibodyModeler.hh
src/protocols/antibody/CDRH3Modeler.ccModels CDR H3 loop using loop modeling
src/protocols/antibody/CDRH3Modeler.hh
src/protocols/antibody/GraftMover.cc
src/protocols/antibody/GraftMover.hh
src/protocols/antibody/Ubiquitin_E2C_Modeler.cc
src/protocols/antibody/Ubiquitin_E2C_Modeler.fwd.hhForward declaration
src/protocols/antibody/Ubiquitin_E2C_Modeler.hhBuild model for di-ubiquitin and e2c enzyme complex
src/protocols/antibody2/Ab_Assemble_Templates.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_Assemble_Templates.fwd.hhForward declaration
src/protocols/antibody2/Ab_Assemble_Templates.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_CloseOneCDR_Mover.ccGrafts a cdr onto the template of an antibody framework
src/protocols/antibody2/Ab_CloseOneCDR_Mover.fwd.hh
src/protocols/antibody2/Ab_CloseOneCDR_Mover.hh
src/protocols/antibody2/Ab_GraftOneCDR_Mover.ccGrafts a cdr onto the template of an antibody framework
src/protocols/antibody2/Ab_GraftOneCDR_Mover.fwd.hh
src/protocols/antibody2/Ab_GraftOneCDR_Mover.hhGrafts a cdr onto the template of an antibody framework
src/protocols/antibody2/Ab_H3_cter_insert_mover.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_H3_cter_insert_mover.fwd.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_H3_cter_insert_mover.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_H3_perturb_ccd_build.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_H3_perturb_ccd_build.fwd.hh
src/protocols/antibody2/Ab_H3_perturb_ccd_build.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_Info.cc
src/protocols/antibody2/Ab_Info.fwd.hhAb_Info class forward declarations header
src/protocols/antibody2/Ab_Info.hh
src/protocols/antibody2/Ab_LH_RepulsiveRamp_Mover.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_LH_RepulsiveRamp_Mover.fwd.hh
src/protocols/antibody2/Ab_LH_RepulsiveRamp_Mover.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_LH_SnugFit_Mover.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_LH_SnugFit_Mover.fwd.hh
src/protocols/antibody2/Ab_LH_SnugFit_Mover.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_ModelCDRH3.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_ModelCDRH3.fwd.hhForward declaration
src/protocols/antibody2/Ab_ModelCDRH3.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_Relax_a_CDR_FullAtom.ccBuild a homology model of an antibody2
src/protocols/antibody2/Ab_Relax_a_CDR_FullAtom.fwd.hh
src/protocols/antibody2/Ab_Relax_a_CDR_FullAtom.hhBuild a homology model of an antibody2
src/protocols/antibody2/Ab_RelaxCDRs_Mover.ccGrafts a cdr onto the template of an antibody framework
src/protocols/antibody2/Ab_RelaxCDRs_Mover.fwd.hh
src/protocols/antibody2/Ab_RelaxCDRs_Mover.hh
src/protocols/antibody2/Ab_TemplateInfo.cc
src/protocols/antibody2/Ab_TemplateInfo.fwd.hh
src/protocols/antibody2/Ab_TemplateInfo.hh
src/protocols/antibody2/Ab_util.cc
src/protocols/antibody2/Ab_util.hh
src/protocols/antibody2/CDRH3Modeler2.ccModels CDR H3 loop using loop modeling
src/protocols/antibody2/CDRH3Modeler2.fwd.hh
src/protocols/antibody2/CDRH3Modeler2.hh
src/protocols/backrub/BackrubMover.ccImplementation of BackrubMover class and functions
src/protocols/backrub/BackrubMover.fwd.hh
src/protocols/backrub/BackrubMover.hhDefinition of BackrubMover class and functions
src/protocols/backrub/BackrubMoverCreator.hhThis class will create instances of Mover BackrubMover for the MoverFactory
src/protocols/backrub/BackrubSegment.ccImplmentation of BackrubSegment class
src/protocols/backrub/BackrubSegment.hhDefinition/implmentation of BackrubSegment class
src/protocols/backrub/BackrubSidechainMover.ccBackrubSidechainMover methods implemented
src/protocols/backrub/BackrubSidechainMover.fwd.hhBackrubSidechainMover forward declarations header
src/protocols/backrub/BackrubSidechainMover.hh
src/protocols/backrub/BackrubSidechainMoverCreator.hhThis class will create instances of Mover BackrubSidechainMover for the MoverFactory
src/protocols/boinc/boinc.ccWrappers to make BOINC work
src/protocols/boinc/boinc.hhWrappers to make BOINC work
src/protocols/boinc/boinc_shmem.hh
src/protocols/boinc/BoincPoseObserver.ccBoincPoseObserver class
src/protocols/boinc/BoincPoseObserver.fwd.hh
src/protocols/boinc/BoincPoseObserver.hhBoincPoseObserver class
src/protocols/boinc/watchdog.cc
src/protocols/boinc/watchdog.hh
src/protocols/branch_angle/BranchAngleOptimizer.cc
src/protocols/branch_angle/BranchAngleOptimizer.fwd.hhBranchAngleOptimizer class forward declaration
src/protocols/branch_angle/BranchAngleOptimizer.hh
src/protocols/branch_angle/BranchCoef1.fwd.hhBranchCoef1 class forward declaration
src/protocols/branch_angle/BranchCoef1.hhDefinition/implementation of BranchCoef1 class and methods
src/protocols/branch_angle/BranchCoef2.fwd.hhBranchCoef2 class forward declaration
src/protocols/branch_angle/BranchCoef2.hhDefinition/implementation of BranchCoef2 class and methods
src/protocols/branch_angle/BranchParam1.fwd.hhBranchParam1 class forward declaration
src/protocols/branch_angle/BranchParam1.hhDefinition/implementation of BranchParam1 class and methods
src/protocols/branch_angle/BranchParam2.fwd.hhBranchParam2 class forward declaration
src/protocols/branch_angle/BranchParam2.hhDefinition/implementation of BranchParam2 class and methods
src/protocols/canonical_sampling/CanonicalSamplingApplication.cc
src/protocols/canonical_sampling/CanonicalSamplingApplication.hh
src/protocols/canonical_sampling/CanonicalSamplingMover.cc
src/protocols/canonical_sampling/CanonicalSamplingMover.fwd.hh
src/protocols/canonical_sampling/CanonicalSamplingMover.hh
src/protocols/canonical_sampling/HamiltonianExchange.cc
src/protocols/canonical_sampling/HamiltonianExchange.fwd.hh
src/protocols/canonical_sampling/HamiltonianExchange.hh
src/protocols/canonical_sampling/HamiltonianExchangeCreator.hhThis class will create instances of Mover HamiltonianExchange for the MoverFactory
src/protocols/canonical_sampling/MetricRecorder.cc
src/protocols/canonical_sampling/MetricRecorder.fwd.hhForward declarations for class MetricRecorder
src/protocols/canonical_sampling/MetricRecorder.hh
src/protocols/canonical_sampling/MetricRecorderCreator.hhThis class will create instances of Mover MetricRecorder for the MoverFactory
src/protocols/canonical_sampling/MetropolisHastingsMover.ccMetropolisHastingsMover methods implemented
src/protocols/canonical_sampling/MetropolisHastingsMover.fwd.hhMetropolisHastingsMover forward declarations header
src/protocols/canonical_sampling/MetropolisHastingsMover.hhImplement replica exchange in the MetropolisHastingsMover Framework
src/protocols/canonical_sampling/MetropolisHastingsMoverCreator.hhThis class will create instances of Mover MetropolisHastingsMover for the MoverFactory
src/protocols/canonical_sampling/MultiTemperatureTrialCounter.cc
src/protocols/canonical_sampling/MultiTemperatureTrialCounter.hh
src/protocols/canonical_sampling/ParallelTempering.cc
src/protocols/canonical_sampling/ParallelTempering.fwd.hh
src/protocols/canonical_sampling/ParallelTempering.hh
src/protocols/canonical_sampling/ParallelTemperingCreator.hhThis class will create instances of Mover ParallelTempering for the MoverFactory
src/protocols/canonical_sampling/PDBTrajectoryRecorder.cc
src/protocols/canonical_sampling/PDBTrajectoryRecorder.fwd.hh
src/protocols/canonical_sampling/PDBTrajectoryRecorder.hh
src/protocols/canonical_sampling/PDBTrajectoryRecorderCreator.hhThis class will create instances of Mover PDBTrajectoryRecorder for the MoverFactory
src/protocols/canonical_sampling/SidechainMetropolisHastingsMover.ccSidechainMetropolisHastingsMover methods implemented
src/protocols/canonical_sampling/SidechainMetropolisHastingsMover.fwd.hh
src/protocols/canonical_sampling/SidechainMetropolisHastingsMover.hh
src/protocols/canonical_sampling/SidechainMetropolisHastingsMoverCreator.hhThis class will create instances of Mover SidechainMetropolisHastingsMover for the MoverFactory
src/protocols/canonical_sampling/SilentTrajectoryRecorder.cc
src/protocols/canonical_sampling/SilentTrajectoryRecorder.fwd.hhForward declarations for class SilentTrajectoryRecorder
src/protocols/canonical_sampling/SilentTrajectoryRecorder.hh
src/protocols/canonical_sampling/SilentTrajectoryRecorderCreator.hhThis class will create instances of Mover SilentTrajectoryRecorder for the MoverFactory
src/protocols/canonical_sampling/SimulatedTempering.cc
src/protocols/canonical_sampling/SimulatedTempering.fwd.hh
src/protocols/canonical_sampling/SimulatedTempering.hh
src/protocols/canonical_sampling/SimulatedTemperingCreator.hhThis class will create instances of Mover SimulatedTempering for the MoverFactory
src/protocols/canonical_sampling/SimulatedTemperingObserver.fwd.hh
src/protocols/canonical_sampling/TemperatureController.cc
src/protocols/canonical_sampling/TemperatureController.fwd.hh
src/protocols/canonical_sampling/TemperatureController.hh
src/protocols/canonical_sampling/TemperingBase.cc
src/protocols/canonical_sampling/TemperingBase.fwd.hh
src/protocols/canonical_sampling/TemperingBase.hh
src/protocols/canonical_sampling/ThermodynamicMover.ccThermodynamicMover methods implemented
src/protocols/canonical_sampling/ThermodynamicMover.fwd.hhThermodynamicMover forward declarations header
src/protocols/canonical_sampling/ThermodynamicMover.hh
src/protocols/canonical_sampling/ThermodynamicObserver.ccThermodynamicObserver methods implemented
src/protocols/canonical_sampling/ThermodynamicObserver.fwd.hhThermodynamicObserver forward declarations header
src/protocols/canonical_sampling/ThermodynamicObserver.hh
src/protocols/canonical_sampling/TrajectoryRecorder.cc
src/protocols/canonical_sampling/TrajectoryRecorder.fwd.hhForward declarations for class TrajectoryRecorder
src/protocols/canonical_sampling/TrajectoryRecorder.hh
src/protocols/canonical_sampling/TrajectoryRecorderCreator.hhThis class will create instances of Mover TrajectoryRecorder for the MoverFactory
src/protocols/canonical_sampling/TrialCounterObserver.ccProtocols::canonical_sampling::TrialCounterObserver methods implemented
src/protocols/canonical_sampling/TrialCounterObserver.hh
src/protocols/canonical_sampling/TrialCounterObserverCreator.hhThis class will create instances of Mover TrialCounterObserver for the MoverFactory
src/protocols/canonical_sampling/mc_convergence_checks/Heat_ConvergenceCheck.hh
src/protocols/canonical_sampling/mc_convergence_checks/HierarchicalLevel.cc
src/protocols/canonical_sampling/mc_convergence_checks/HierarchicalLevel.fwd.hh
src/protocols/canonical_sampling/mc_convergence_checks/HierarchicalLevel.hh
src/protocols/canonical_sampling/mc_convergence_checks/HPool.ccHierarchical pool
src/protocols/canonical_sampling/mc_convergence_checks/HPool.fwd.hhHierarchical pool
src/protocols/canonical_sampling/mc_convergence_checks/HPool.hhHierarchical pool
src/protocols/canonical_sampling/mc_convergence_checks/MPIBPool_ConvergenceCheck.cc
src/protocols/canonical_sampling/mc_convergence_checks/MPIBPool_ConvergenceCheck.fwd.hh
src/protocols/canonical_sampling/mc_convergence_checks/MPIBPool_ConvergenceCheck.hh
src/protocols/canonical_sampling/mc_convergence_checks/MPIHPool_ConvergenceCheck.cc
src/protocols/canonical_sampling/mc_convergence_checks/MPIHPool_ConvergenceCheck.fwd.hh
src/protocols/canonical_sampling/mc_convergence_checks/MPIHPool_ConvergenceCheck.hh
src/protocols/canonical_sampling/mc_convergence_checks/MPIPool_ConvergenceCheck.cc
src/protocols/canonical_sampling/mc_convergence_checks/MPIPool_ConvergenceCheck.fwd.hh
src/protocols/canonical_sampling/mc_convergence_checks/MPIPool_ConvergenceCheck.hh
src/protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.cc
src/protocols/canonical_sampling/mc_convergence_checks/Pool_ConvergenceCheck.hh
src/protocols/canonical_sampling/mc_convergence_checks/pool_util.cc
src/protocols/canonical_sampling/mc_convergence_checks/pool_util.hh
src/protocols/canonical_sampling/mc_convergence_checks/util.cc
src/protocols/canonical_sampling/mc_convergence_checks/util.hh
src/protocols/cartesian/md.cc
src/protocols/cartesian/md.hh
src/protocols/checkpoint/Checkpoint.cc
src/protocols/checkpoint/Checkpoint.fwd.hh
src/protocols/checkpoint/Checkpoint.hh
src/protocols/checkpoint/CheckPointer.cc
src/protocols/checkpoint/CheckPointer.fwd.hh
src/protocols/checkpoint/CheckPointer.hh
src/protocols/cluster/APCluster.cc
src/protocols/cluster/APCluster.fwd.hh
src/protocols/cluster/APCluster.hh
src/protocols/cluster/cluster.cc
src/protocols/cluster/cluster.hh
src/protocols/coarse_rna/CoarseRNA_DeNovoProtocol.cc
src/protocols/coarse_rna/CoarseRNA_DeNovoProtocol.hh
src/protocols/coarse_rna/CoarseRNA_Fragments.cc
src/protocols/coarse_rna/CoarseRNA_Fragments.hh
src/protocols/coarse_rna/CoarseRNA_LoopCloser.cc
src/protocols/coarse_rna/CoarseRNA_LoopCloser.fwd.hh
src/protocols/coarse_rna/CoarseRNA_LoopCloser.hh
src/protocols/comparative_modeling/Align_RmsdEvaluator.cc
src/protocols/comparative_modeling/Align_RmsdEvaluator.fwd.hhForward declaration for Align_RmsdEvaluator class
src/protocols/comparative_modeling/Align_RmsdEvaluator.hh
src/protocols/comparative_modeling/Align_RotamerEvaluator.cc
src/protocols/comparative_modeling/Align_RotamerEvaluator.fwd.hhForward declaration for Align_RotamerEvaluator class
src/protocols/comparative_modeling/Align_RotamerEvaluator.hh
src/protocols/comparative_modeling/AlignmentClustering.cc
src/protocols/comparative_modeling/AlignmentClustering.fwd.hh
src/protocols/comparative_modeling/AlignmentClustering.hhDivide input alns into clusters based on gdtmm comparison of partial models. Uses the top e-value or hh-value sample as the cluster center
src/protocols/comparative_modeling/AlignmentID.hh
src/protocols/comparative_modeling/AlignmentSet.cc
src/protocols/comparative_modeling/AlignmentSet.fwd.hhForward declaration for AlignmentSet class
src/protocols/comparative_modeling/AlignmentSet.hh
src/protocols/comparative_modeling/AlignRmsdTargetEvaluatorCreator.cc
src/protocols/comparative_modeling/AlignRmsdTargetEvaluatorCreator.hhHeader for AlignRmsdTargetEvaluatorCreator
src/protocols/comparative_modeling/cm_main.cc
src/protocols/comparative_modeling/cm_main.hh
src/protocols/comparative_modeling/coord_util.cc
src/protocols/comparative_modeling/coord_util.hh
src/protocols/comparative_modeling/ExtraThreadingMover.ccMethod declarations for ExtraThreadingMover
src/protocols/comparative_modeling/ExtraThreadingMover.hhClass for copying extra stuff (ligands,dna,peptides,etc) from a template Pose
src/protocols/comparative_modeling/GenericJobInputter.cc
src/protocols/comparative_modeling/GenericJobInputter.fwd.hhHeader file for ThreadingJobInputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/comparative_modeling/GenericJobInputter.hh
src/protocols/comparative_modeling/GenericJobInputterCreator.hh
src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.cc
src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.fwd.hhForward declaration for IgnoreSubsetConstraintSet class
src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.hh
src/protocols/comparative_modeling/LoopRelaxMover.cc
src/protocols/comparative_modeling/LoopRelaxMover.fwd.hhForward declaration for LoopRelaxMover class
src/protocols/comparative_modeling/LoopRelaxMover.hh
src/protocols/comparative_modeling/LoopRelaxMoverCreator.hh
src/protocols/comparative_modeling/LoopRelaxThreadingMover.cc
src/protocols/comparative_modeling/LoopRelaxThreadingMover.fwd.hhForward declaration for LoopRelaxThreadingMover class
src/protocols/comparative_modeling/LoopRelaxThreadingMover.hh
src/protocols/comparative_modeling/MultiThreadingMover.cc
src/protocols/comparative_modeling/MultiThreadingMover.hh
src/protocols/comparative_modeling/PartialThreadingMover.cc
src/protocols/comparative_modeling/PartialThreadingMover.hh
src/protocols/comparative_modeling/RecoverSideChainsMover.cc
src/protocols/comparative_modeling/RecoverSideChainsMover.fwd.hhForward declaration for RecoverSideChainsMover class
src/protocols/comparative_modeling/RecoverSideChainsMover.hh
src/protocols/comparative_modeling/StealLigandMover.cc
src/protocols/comparative_modeling/StealLigandMover.fwd.hhForward declaration for StealLigandMover class
src/protocols/comparative_modeling/StealLigandMover.hh
src/protocols/comparative_modeling/StealSideChainsMover.cc
src/protocols/comparative_modeling/StealSideChainsMover.fwd.hhForward declaration for StealSideChainsMover class
src/protocols/comparative_modeling/StealSideChainsMover.hh
src/protocols/comparative_modeling/ThreadingJob.cc
src/protocols/comparative_modeling/ThreadingJob.fwd.hhHeader file for ThreadingJob classes
src/protocols/comparative_modeling/ThreadingJob.hhHeader file for ThreadingJob classes
src/protocols/comparative_modeling/ThreadingJobInputter.cc
src/protocols/comparative_modeling/ThreadingJobInputter.fwd.hh
src/protocols/comparative_modeling/ThreadingJobInputter.hh
src/protocols/comparative_modeling/ThreadingJobInputterCreator.hh
src/protocols/comparative_modeling/ThreadingMover.ccMethod declarations for ThreadingMover
src/protocols/comparative_modeling/ThreadingMover.hh
src/protocols/comparative_modeling/util.ccSet of utilities used in comparative modeling of protein structures
src/protocols/comparative_modeling/util.hhSmall bundle of utilities for comparative modeling
src/protocols/comparative_modeling/features/ResidueFeature.cc
src/protocols/comparative_modeling/features/ResidueFeature.fwd.hhForward declaration for ResidueFeature class
src/protocols/comparative_modeling/features/ResidueFeature.hhAbstract base class for per-residue features used in comparative modeling
src/protocols/comparative_modeling/features/ResidueFeatureFactory.ccFactory for creating various types of ResidueFeatures
src/protocols/comparative_modeling/features/ResidueFeatureFactory.hh
src/protocols/comparative_modeling/features/SSFeature.cc
src/protocols/comparative_modeling/features/SSFeature.fwd.hhForward declaration for SSFeature class
src/protocols/comparative_modeling/features/SSFeature.hh
src/protocols/comparative_modeling/features/TorsionFeature.cc
src/protocols/comparative_modeling/features/TorsionFeature.fwd.hhForward declaration for TorsionFeature class
src/protocols/comparative_modeling/features/TorsionFeature.hh
src/protocols/comparative_modeling/hybridize/CartesianHybridize.cc
src/protocols/comparative_modeling/hybridize/CartesianHybridize.fwd.hh
src/protocols/comparative_modeling/hybridize/CartesianHybridize.hh
src/protocols/comparative_modeling/hybridize/ChunkTrialMover.ccWrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one
src/protocols/comparative_modeling/hybridize/ChunkTrialMover.fwd.hh
src/protocols/comparative_modeling/hybridize/ChunkTrialMover.hhWrapper for InsertChunkMover. It can take a random template and steal coordinates of all chunks or a random one
src/protocols/comparative_modeling/hybridize/FoldTreeHybridize.ccAlign a random jump to template
src/protocols/comparative_modeling/hybridize/FoldTreeHybridize.fwd.hh
src/protocols/comparative_modeling/hybridize/FoldTreeHybridize.hhAlign a random jump to template
src/protocols/comparative_modeling/hybridize/HybridizeFoldtreeDynamic.ccA mover to dynamically manipulate fold tree during the template hybridization sampling
src/protocols/comparative_modeling/hybridize/HybridizeFoldtreeDynamic.fwd.hh
src/protocols/comparative_modeling/hybridize/HybridizeFoldtreeDynamic.hh
src/protocols/comparative_modeling/hybridize/HybridizeProtocol.cc
src/protocols/comparative_modeling/hybridize/HybridizeProtocol.fwd.hh
src/protocols/comparative_modeling/hybridize/HybridizeProtocol.hhAdd constraints to the current pose conformation
src/protocols/comparative_modeling/hybridize/HybridizeProtocolCreator.hh
src/protocols/comparative_modeling/hybridize/InsertChunkMover.ccAlign a random jump to template
src/protocols/comparative_modeling/hybridize/InsertChunkMover.hhAlign a random jump to template
src/protocols/comparative_modeling/hybridize/TemplateHistory.cc
src/protocols/comparative_modeling/hybridize/TemplateHistory.fwd.hh
src/protocols/comparative_modeling/hybridize/TemplateHistory.hh
src/protocols/comparative_modeling/hybridize/util.ccAlign a random jump to template
src/protocols/comparative_modeling/hybridize/util.hhAlign a random jump to template
src/protocols/comparative_modeling/hybridize/WeightedFragmentTrialMover.ccFragment insertion and trial, each residue has a customized weight for the frequency of insertion
src/protocols/comparative_modeling/hybridize/WeightedFragmentTrialMover.fwd.hh
src/protocols/comparative_modeling/hybridize/WeightedFragmentTrialMover.hhFragment insertion and trial, each residue has a customized weight for the frequency of insertion
src/protocols/constraints_additional/AdditionalConstraintCreators.cc
src/protocols/constraints_additional/AdditionalConstraintCreators.hh
src/protocols/constraints_additional/AmbiguousMultiConstraint.ccDeclarations for a type of constraint that holds a number of constraints
src/protocols/constraints_additional/AmbiguousMultiConstraint.fwd.hh
src/protocols/constraints_additional/AmbiguousMultiConstraint.hhDeclarations for a type of constraint that holds multiple other
src/protocols/constraints_additional/BindingSiteConstraint.cc
src/protocols/constraints_additional/BindingSiteConstraint.hh
src/protocols/constraints_additional/CombinedConstraintEvaluator.cc
src/protocols/constraints_additional/CombinedConstraintEvaluator.hh
src/protocols/constraints_additional/CombinedConstraintEvaluatorCreator.cc
src/protocols/constraints_additional/CombinedConstraintEvaluatorCreator.hh
src/protocols/constraints_additional/ConstraintEvaluator.cc
src/protocols/constraints_additional/ConstraintEvaluator.fwd.hh
src/protocols/constraints_additional/ConstraintEvaluator.hh
src/protocols/constraints_additional/ConstraintEvaluatorCreator.cc
src/protocols/constraints_additional/ConstraintEvaluatorCreator.hh
src/protocols/constraints_additional/MaxSeqSepConstraintSet.cc
src/protocols/constraints_additional/MaxSeqSepConstraintSet.fwd.hh
src/protocols/constraints_additional/MaxSeqSepConstraintSet.hhHelper class for FoldConstraints Protocol, filters constraints by sequence separation
src/protocols/constraints_additional/SequenceCoupling1BDConstraint.cc
src/protocols/constraints_additional/SequenceCoupling1BDConstraint.fwd.hhThis is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design)
src/protocols/constraints_additional/SequenceCoupling1BDConstraint.hhThis is a constraint that refers to a core::sequence::SequenceCoupling1BD? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design)
src/protocols/constraints_additional/SequenceCouplingConstraint.cc
src/protocols/constraints_additional/SequenceCouplingConstraint.fwd.hhThis is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design)
src/protocols/constraints_additional/SequenceCouplingConstraint.hhThis is a constraint that refers to a core::sequence::SequenceCoupling? in order to influence the scoring of amino acid types based on multiple sequence alignments (i.e. for biasing amino acid choices during design)
src/protocols/contact_map/ContactMap.ccMethod code and full headers for ContactMapCreator, ContactMap, ContactPartner and contact
src/protocols/contact_map/ContactMap.fwd.hh
src/protocols/contact_map/ContactMap.hhMover to create a ContactMap
src/protocols/contact_map/ContactMapCreator.hh
src/protocols/ddg/ddG_main.cc
src/protocols/ddg/ddG_main.hh
src/protocols/ddg/ddGData.cc
src/protocols/ddg/ddGData.fwd.hh
src/protocols/ddg/ddGData.hh
src/protocols/ddg/ddGMover.cc
src/protocols/ddg/ddGMover.hh
src/protocols/dna/DesignProteinBackboneAroundDNA.ccPerforms a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.)
src/protocols/dna/DesignProteinBackboneAroundDNA.fwd.hh
src/protocols/dna/DesignProteinBackboneAroundDNA.hhPerforms a round flexible backbone sampling/design. (Interim(?) encapsulation of some loose code in a mover class.)
src/protocols/dna/DesignProteinBackboneAroundDNACreator.hh
src/protocols/dna/DnaChains.cc
src/protocols/dna/DnaChains.fwd.hh
src/protocols/dna/DnaChains.hhDescriptive but lightweight class to keep track of (usually basepaired) dna chains
src/protocols/dna/DnaDesignDef.cc
src/protocols/dna/DnaDesignDef.fwd.hh
src/protocols/dna/DnaDesignDef.hh
src/protocols/dna/DnaInterfaceFinder.cc
src/protocols/dna/DnaInterfaceFinder.fwd.hh
src/protocols/dna/DnaInterfaceFinder.hh
src/protocols/dna/DnaInterfaceMinMover.cc
src/protocols/dna/DnaInterfaceMinMover.fwd.hh
src/protocols/dna/DnaInterfaceMinMover.hhA mover that minimizes protein residues near DNA
src/protocols/dna/DnaInterfaceMinMoverCreator.hh
src/protocols/dna/DnaInterfaceMultiStateDesign.cc
src/protocols/dna/DnaInterfaceMultiStateDesign.fwd.hh
src/protocols/dna/DnaInterfaceMultiStateDesign.hh
src/protocols/dna/DnaInterfaceMultiStateDesignCreator.hh
src/protocols/dna/DnaInterfacePacker.cc
src/protocols/dna/DnaInterfacePacker.fwd.hh
src/protocols/dna/DnaInterfacePacker.hhIntended to perform anything one would want to do in a DNA interface that uses a single incarnation of the RotamerSets/InteractionGraph combo
src/protocols/dna/DnaInterfacePackerCreator.hh
src/protocols/dna/PDBOutput.cc
src/protocols/dna/PDBOutput.fwd.hh
src/protocols/dna/PDBOutput.hh
src/protocols/dna/RestrictDesignToProteinDNAInterface.cc
src/protocols/dna/RestrictDesignToProteinDNAInterface.fwd.hh
src/protocols/dna/RestrictDesignToProteinDNAInterface.hhWhen operated on a PackerTask, pack/design is limited to the protein-DNA interface
src/protocols/dna/RestrictDesignToProteinDNAInterfaceCreator.hh
src/protocols/dna/RotamerDNAHBondFilter.ccFilters rotamers for contact to DNA in an -ex dependent manner
src/protocols/dna/RotamerDNAHBondFilter.fwd.hh
src/protocols/dna/RotamerDNAHBondFilter.hhFilters rotamers for contact to DNA in an -ex dependent manner
src/protocols/dna/SeparateDnaFromNonDna.cc
src/protocols/dna/SeparateDnaFromNonDna.fwd.hh
src/protocols/dna/SeparateDnaFromNonDna.hh
src/protocols/dna/SeparateDnaFromNonDnaCreator.hh
src/protocols/dna/typedefs.hh
src/protocols/dna/util.cc
src/protocols/dna/util.hh
src/protocols/dna/WatsonCrickRotamerCouplings.cc
src/protocols/dna/WatsonCrickRotamerCouplings.fwd.hh
src/protocols/dna/WatsonCrickRotamerCouplings.hhWhen operated on a PackerTask, adds RotamerCouplings to it that will trigger the use of a FixbbCoupledRotamerAnnealer by pack_rotamers, which will make base-paired DNA rotamer substitutions
src/protocols/dna/WatsonCrickRotamerCouplingsCreator.hh
src/protocols/docking/ConformerSwitchMover.ccCode for the conformer switch mover in ensemble docking
src/protocols/docking/ConformerSwitchMover.fwd.hhConformerSwitchMover forward declarations header
src/protocols/docking/ConformerSwitchMover.hh
src/protocols/docking/ConformerSwitchMoverCreator.hh
src/protocols/docking/DockFilters.cc
src/protocols/docking/DockFilters.fwd.hh
src/protocols/docking/DockFilters.hh
src/protocols/docking/DockingEnsemble.ccContainer class for ensemble docking information to be used with ConformerSwitchMover
src/protocols/docking/DockingEnsemble.fwd.hh
src/protocols/docking/DockingEnsemble.hh
src/protocols/docking/DockingEnsemblePrepackProtocol.ccPrepacking of the bound structure before docking with ensembles
src/protocols/docking/DockingEnsemblePrepackProtocol.fwd.hh
src/protocols/docking/DockingEnsemblePrepackProtocol.hh
src/protocols/docking/DockingHighRes.cc
src/protocols/docking/DockingHighRes.fwd.hh
src/protocols/docking/DockingHighRes.hh
src/protocols/docking/DockingHighResLegacy.cc
src/protocols/docking/DockingHighResLegacy.fwd.hhForward declarations for DockingHighResLegacy (high resolution docking protocol as it existed in mini before the GrayLab refactor)
src/protocols/docking/DockingHighResLegacy.hh
src/protocols/docking/DockingInitialPerturbation.ccInitial position functions
src/protocols/docking/DockingInitialPerturbation.fwd.hh
src/protocols/docking/DockingInitialPerturbation.hh
src/protocols/docking/DockingLowRes.cc
src/protocols/docking/DockingLowRes.fwd.hh
src/protocols/docking/DockingLowRes.hh
src/protocols/docking/DockingPrepackProtocol.ccPrepacking of the bound sturcture before docking
src/protocols/docking/DockingPrepackProtocol.fwd.hh
src/protocols/docking/DockingPrepackProtocol.hh
src/protocols/docking/DockingProtocol.cc
src/protocols/docking/DockingProtocol.fwd.hh
src/protocols/docking/DockingProtocol.hh
src/protocols/docking/DockingProtocolCreator.hh
src/protocols/docking/DockMCMCycle.cc
src/protocols/docking/DockMCMCycle.fwd.hhForward declarations for DockMCMCycle (high resolution min) docking
src/protocols/docking/DockMCMCycle.hh
src/protocols/docking/DockMCMProtocol.cc
src/protocols/docking/DockMCMProtocol.fwd.hhForward declarations for DockMCMProtocol (high resolution min) docking
src/protocols/docking/DockMCMProtocol.hh
src/protocols/docking/DockMinMover.cc
src/protocols/docking/DockMinMover.fwd.hhForward declarations for DockMinMover (high resolution min) docking
src/protocols/docking/DockMinMover.hh
src/protocols/docking/DockSetupMover.cc
src/protocols/docking/DockSetupMover.fwd.hh
src/protocols/docking/DockSetupMover.hh
src/protocols/docking/DockSetupMoverCreator.hh
src/protocols/docking/DockTaskFactory.cc
src/protocols/docking/DockTaskFactory.fwd.hhForward declarations for DockTaskFactory
src/protocols/docking/DockTaskFactory.hh
src/protocols/docking/metrics.cc
src/protocols/docking/metrics.hh
src/protocols/docking/SidechainMinMover.cc
src/protocols/docking/SidechainMinMover.fwd.hh
src/protocols/docking/SidechainMinMover.hh
src/protocols/docking/TemperedDocking.cc
src/protocols/docking/TemperedDocking.fwd.hh
src/protocols/docking/TemperedDocking.hhAllows low-resolution docking using simulated or parallel tempering
src/protocols/docking/TemperedDockingCreator.hh
src/protocols/docking/types.hhAdditionl types for Docking protocol
src/protocols/docking/util.cc
src/protocols/docking/util.hh
src/protocols/docking/stateless/SaneDockingProtocol.cc
src/protocols/docking/stateless/SaneDockingProtocol.fwd.hh
src/protocols/docking/stateless/SaneDockingProtocol.hhDockingProtocol class that doesn't use the more esoteric features of the Mover base class (e.g get_input_pose())
src/protocols/domain_assembly/AddAssemblyConstraints.cc
src/protocols/domain_assembly/AddAssemblyConstraints.fwd.hhAdds constraints for the assembling process
src/protocols/domain_assembly/AddAssemblyConstraints.hh
src/protocols/domain_assembly/AssembleLinkerMover.ccA mover for assembling domains
src/protocols/domain_assembly/AssembleLinkerMover.fwd.hhA mover for assembling domains
src/protocols/domain_assembly/AssembleLinkerMover.hh
src/protocols/domain_assembly/CombineChainsMover.ccTakes a multichain pose and returns a single-chain one
src/protocols/domain_assembly/CombineChainsMover.fwd.hhA mover for assembling chains
src/protocols/domain_assembly/CombineChainsMover.hh
src/protocols/domain_assembly/PostDockAssemblyScorer.ccComputes crmsd of the assembly to the staring point
src/protocols/domain_assembly/PostDockAssemblyScorer.fwd.hhComputes crmsd of the assembly to the staring point
src/protocols/domain_assembly/PostDockAssemblyScorer.hh
src/protocols/electron_density/SetupForDensityScoringMover.ccProtocols for folding into density
src/protocols/electron_density/SetupForDensityScoringMover.hhProtocols for folding into density
src/protocols/electron_density/SetupForDensityScoringMoverCreator.hh
src/protocols/electron_density/util.ccProtocols for folding into density
src/protocols/electron_density/util.hhProtocols for folding into density
src/protocols/enzdes/AddLigandMotifRotamersOperationCreator.hh
src/protocols/enzdes/AddorRemoveCsts.cc
src/protocols/enzdes/AddorRemoveCsts.hh
src/protocols/enzdes/AddOrRemoveMatchCstsCreator.hh
src/protocols/enzdes/AddRigidBodyLigandConfsCreator.hh
src/protocols/enzdes/BackboneSampler.cc
src/protocols/enzdes/BackboneSampler.hhAdapted from backrub mover in protein interface design
src/protocols/enzdes/BackboneSamplerCreator.hh
src/protocols/enzdes/DesignVsNativeComparison.cc
src/protocols/enzdes/DesignVsNativeComparison.hh
src/protocols/enzdes/DetectProteinLigandInterfaceOperationCreator.hh
src/protocols/enzdes/enzdes_util.ccBunch of utility functions used in enzdes
src/protocols/enzdes/enzdes_util.hhBunch of utility functions used in enzdes
src/protocols/enzdes/EnzdesBaseProtocol.cc
src/protocols/enzdes/EnzdesBaseProtocol.fwd.hh
src/protocols/enzdes/EnzdesBaseProtocol.hh
src/protocols/enzdes/EnzdesFixBBProtocol.cc
src/protocols/enzdes/EnzdesFixBBProtocol.hh
src/protocols/enzdes/EnzdesFlexBBProtocol.cc
src/protocols/enzdes/EnzdesFlexBBProtocol.hh
src/protocols/enzdes/EnzdesJobInputter.ccJob inputter that adds some stuff for enzdes to the pose
src/protocols/enzdes/EnzdesJobInputter.fwd.hh
src/protocols/enzdes/EnzdesJobInputter.hh
src/protocols/enzdes/EnzdesJobInputterCreator.hh
src/protocols/enzdes/EnzdesJobOutputter.ccImplementation for EnzdesJobOutputter
src/protocols/enzdes/EnzdesJobOutputter.fwd.hhForward declaration for EnzdesJobOutputters
src/protocols/enzdes/EnzdesJobOutputter.hh
src/protocols/enzdes/EnzdesJobOutputterCreator.hh
src/protocols/enzdes/EnzdesMovers.cc
src/protocols/enzdes/EnzdesMovers.fwd.hh
src/protocols/enzdes/EnzdesMovers.hhCollection of movers that are used at different stages in enzyme design
src/protocols/enzdes/EnzdesMoversCreator.hh
src/protocols/enzdes/EnzdesTaskOperations.cc
src/protocols/enzdes/EnzdesTaskOperations.fwd.hh
src/protocols/enzdes/EnzdesTaskOperations.hh
src/protocols/enzdes/EnzFilterCreators.hhFilterCreators for the enzyme design filters
src/protocols/enzdes/EnzFilters.cc
src/protocols/enzdes/EnzFilters.fwd.hh
src/protocols/enzdes/EnzFilters.hhDefinition of filter classes for enzdes in rosetta_scripts framework
src/protocols/enzdes/EnzRepackMinimize.ccRepack/minimize class for rosetta_scripts-compatible enzdes
src/protocols/enzdes/EnzRepackMinimize.fwd.hh
src/protocols/enzdes/EnzRepackMinimize.hh
src/protocols/enzdes/EnzRepackMinimizeCreator.hh
src/protocols/enzdes/ModifyStoredLigandRBConfsMovers.cc
src/protocols/enzdes/ModifyStoredLigandRBConfsMovers.fwd.hh
src/protocols/enzdes/ModifyStoredLigandRBConfsMovers.hh
src/protocols/enzdes/ProteinLigandInterfaceUpweighterOperationCreator.hh
src/protocols/enzdes/SecondaryMatchProtocol.cc
src/protocols/enzdes/SecondaryMatchProtocol.hh
src/protocols/enzdes/SetCatalyticResPackBehaviorCreator.hh
src/protocols/evaluation/AlignEvaluator.cc
src/protocols/evaluation/AlignEvaluator.fwd.hhForward declaration for AlignEvaluator class
src/protocols/evaluation/AlignEvaluator.hh
src/protocols/evaluation/EvaluatorCreator.fwd.hhForward Header for base class for EvaluatorCreators for the Evaluator load-time factory registration scheme
src/protocols/evaluation/EvaluatorCreator.hh
src/protocols/evaluation/EvaluatorFactory.ccFactory for creating Evaluators objects
src/protocols/evaluation/EvaluatorFactory.fwd.hhReport data to database
src/protocols/evaluation/EvaluatorFactory.hhFactory for creating Evaluator objects
src/protocols/evaluation/PCA.cc
src/protocols/evaluation/PCA.fwd.hh
src/protocols/evaluation/PCA.hh
src/protocols/evaluation/PoseEvaluator.cc
src/protocols/evaluation/PoseEvaluator.fwd.hh
src/protocols/evaluation/PoseEvaluator.hh
src/protocols/evaluation/TimeEvaluator.cc
src/protocols/evaluation/TimeEvaluator.fwd.hh
src/protocols/evaluation/TimeEvaluator.hh
src/protocols/evaluation/util.cc
src/protocols/evaluation/util.hh
src/protocols/features/AtomAtomPairFeatures.ccReport atom-atom pair geometry and scores to features statistics scientific benchmark
src/protocols/features/AtomAtomPairFeatures.fwd.hhReport atom-atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/AtomAtomPairFeatures.hhReport atom-atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/AtomAtomPairFeaturesCreator.cc
src/protocols/features/AtomAtomPairFeaturesCreator.hhHeader for AtomAtomPairFeaturesCreator for the AtomAtomPairFeatures load-time factory registration scheme
src/protocols/features/AtomInResidueAtomInResiduePairFeatures.ccReport atom-atom pair geometry and scores to features statistics scientific benchmark
src/protocols/features/AtomInResidueAtomInResiduePairFeatures.fwd.hhReport atom-atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/AtomInResidueAtomInResiduePairFeatures.hhReport atom-atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/AtomInResidueAtomInResiduePairFeaturesCreator.cc
src/protocols/features/AtomInResidueAtomInResiduePairFeaturesCreator.hhHeader for AtomInResidueAtomInResiduePairFeaturesCreator for the AtomInResidueAtomInResiduePairFeatures load-time factory registration scheme
src/protocols/features/AtomTypesFeatures.ccReport AtomType properties to features Statistics Scientific Benchmark
src/protocols/features/AtomTypesFeatures.fwd.hhReport AtomTypes geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/AtomTypesFeatures.hhReport AtomType features Statistics Scientific Benchmark
src/protocols/features/AtomTypesFeaturesCreator.cc
src/protocols/features/AtomTypesFeaturesCreator.hhHeader for AtomTypesFeaturesCreator for the AtomTypesFeatures load-time factory registration scheme
src/protocols/features/BetaTurnDetectionFeatures.ccReport comments stored with each pose
src/protocols/features/BetaTurnDetectionFeatures.fwd.hhReport residue level geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/BetaTurnDetectionFeatures.hh
src/protocols/features/BetaTurnDetectionFeaturesCreator.cc
src/protocols/features/BetaTurnDetectionFeaturesCreator.hhHeader for BetaTurnDetectionFeaturesCreator for the BetaTurnDetectionFeatures load-time factory registration scheme
src/protocols/features/DatabaseFilters.cc
src/protocols/features/DatabaseFilters.fwd.hhReport data to database
src/protocols/features/DatabaseFilters.hhReport atom-atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/DatabaseJobInputter.cc
src/protocols/features/DatabaseJobInputter.fwd.hh
src/protocols/features/DatabaseJobInputter.hhHeader file for DatabaseJobInputter class
src/protocols/features/DatabaseJobInputterCreator.hh
src/protocols/features/DatabaseJobOutputter.ccJob Outputter to a database
src/protocols/features/DatabaseJobOutputter.fwd.hhHeader file for DatabaseJobOutputter class
src/protocols/features/DatabaseJobOutputter.hhHeader file for DatabaseJobOutputter class
src/protocols/features/DatabaseJobOutputterCreator.hh
src/protocols/features/DatabaseStatements.cc
src/protocols/features/DatabaseStatements.hh
src/protocols/features/FeatureReporterCreator.fwd.hh
src/protocols/features/FeatureReporterCreator.hh
src/protocols/features/FeaturesReporter.ccBase class to report geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/FeaturesReporter.fwd.hhReport data to database
src/protocols/features/FeaturesReporter.hhBase class to report geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/FeaturesReporterCreator.fwd.hh
src/protocols/features/FeaturesReporterCreator.hh
src/protocols/features/FeaturesReporterFactory.ccFactory for creating FeaturesReporters objects
src/protocols/features/FeaturesReporterFactory.fwd.hhReport data to database
src/protocols/features/FeaturesReporterFactory.hhFactory for creating FeaturesReporter objects
src/protocols/features/GeometricSolvationFeatures.ccReport geometric solvation energy for each polar site to a features database
src/protocols/features/GeometricSolvationFeatures.fwd.hhReport geometric solvation for each polar site to features Statistics Scientific Benchmark
src/protocols/features/GeometricSolvationFeatures.hhReport comments stored with each pose
src/protocols/features/GeometricSolvationFeaturesCreator.cc
src/protocols/features/GeometricSolvationFeaturesCreator.hhHeader for GeometricSolvationFeaturesCreator for the GeometricSolvationFeatures load-time factory registration scheme
src/protocols/features/HBondFeatures.ccReport HBond geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/HBondFeatures.fwd.hhReport HBond geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/HBondFeatures.hhReport HBond geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/HBondFeaturesCreator.cc
src/protocols/features/HBondFeaturesCreator.hhHeader for HBondFeaturesCreator for the HBondFeatures load-time factory registration scheme
src/protocols/features/HBondParameterFeatures.ccReport HBond Parameters to features Statistics Scientific Benchmark
src/protocols/features/HBondParameterFeatures.fwd.hhReport HBondParameter geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/HBondParameterFeatures.hhReport HBond Parameter features Statistics Scientific Benchmark
src/protocols/features/HBondParameterFeaturesCreator.cc
src/protocols/features/HBondParameterFeaturesCreator.hhHeader for HBondParameterFeaturesCreator for the HBondParameterFeatures load-time factory registration scheme
src/protocols/features/JobDataFeatures.cc
src/protocols/features/JobDataFeatures.fwd.hh
src/protocols/features/JobDataFeatures.hh
src/protocols/features/JobDataFeaturesCreator.cc
src/protocols/features/JobDataFeaturesCreator.hhHeader for JobDataFeaturesCreator for the JobDataFeatures load-time factory registration scheme
src/protocols/features/LoopAnchorFeatures.ccReport comments stored with each pose
src/protocols/features/LoopAnchorFeatures.fwd.hhReport residue level geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/LoopAnchorFeatures.hhReport comments stored with each pose
src/protocols/features/LoopAnchorFeaturesCreator.cc
src/protocols/features/LoopAnchorFeaturesCreator.hhHeader for LoopAnchorFeaturesCreator for the LoopAnchorFeatures load-time factory registration scheme
src/protocols/features/OrbitalsFeatures.ccReport orbital geometry and scores to features statistics scientific benchmark
src/protocols/features/OrbitalsFeatures.fwd.hhReport Orbital geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/OrbitalsFeatures.hhReport Orbital geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/OrbitalsFeaturesCreator.cc
src/protocols/features/OrbitalsFeaturesCreator.hhHeader for OrbitalsFeaturesCreator for the OrbitalsFeatures load-time factory registration scheme
src/protocols/features/PairFeatures.ccReport orbital geometry and scores to features statistics scientific benchmark
src/protocols/features/PairFeatures.fwd.hhReport atom-atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/PairFeatures.hhReport residue and atom pair geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/PairFeaturesCreator.cc
src/protocols/features/PairFeaturesCreator.hhHeader for PairFeaturesCreator for the PairFeatures load-time factory registration scheme
src/protocols/features/PdbDataFeatures.cc
src/protocols/features/PdbDataFeatures.fwd.hh
src/protocols/features/PdbDataFeatures.hh
src/protocols/features/PdbDataFeaturesCreator.cc
src/protocols/features/PdbDataFeaturesCreator.hhHeader for PdbDataFeaturesCreator for the PdbDataFeatures load-time factory registration scheme
src/protocols/features/PoseCommentsFeatures.ccReport comments stored with each pose
src/protocols/features/PoseCommentsFeatures.fwd.hhReport residue level geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/PoseCommentsFeatures.hhReport comments stored with each pose
src/protocols/features/PoseCommentsFeaturesCreator.cc
src/protocols/features/PoseCommentsFeaturesCreator.hhHeader for PoseCommentsFeaturesCreator for the PoseCommentsFeatures load-time factory registration scheme
src/protocols/features/PoseConformationFeatures.ccReport comments stored with each pose
src/protocols/features/PoseConformationFeatures.fwd.hhReport pose fold tree related features
src/protocols/features/PoseConformationFeatures.hhReport comments stored with each pose
src/protocols/features/PoseConformationFeaturesCreator.cc
src/protocols/features/PoseConformationFeaturesCreator.hhHeader for PoseConformationFeaturesCreator for the PoseConformationFeatures load-time factory registration scheme
src/protocols/features/ProteinBackboneAtomAtomPairFeatures.ccReport atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark
src/protocols/features/ProteinBackboneAtomAtomPairFeatures.fwd.hhReport atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark
src/protocols/features/ProteinBackboneAtomAtomPairFeatures.hhReport atom-atom pair distances between atoms in protein backbones to features Statistics Scientific Benchmark
src/protocols/features/ProteinBackboneAtomAtomPairFeaturesCreator.cc
src/protocols/features/ProteinBackboneAtomAtomPairFeaturesCreator.hhHeader for ProteinBackboneAtomAtomPairFeaturesCreator for the ProteinBackboneAtomAtomPairFeatures load-time factory registration scheme
src/protocols/features/ProteinBackboneTorsionAngleFeatures.ccReport Backbone Torsional Angle features
src/protocols/features/ProteinBackboneTorsionAngleFeatures.fwd.hhReport protein backbone torsion angle features
src/protocols/features/ProteinBackboneTorsionAngleFeatures.hhReport protein backbone torsion angle features
src/protocols/features/ProteinBackboneTorsionAngleFeaturesCreator.cc
src/protocols/features/ProteinBackboneTorsionAngleFeaturesCreator.hhHeader for ProteinBackboneTorsionAngleFeaturesCreator for the ProteinBackboneTorsionAngleFeatures load-time factory registration scheme
src/protocols/features/ProteinResidueConformationFeatures.ccReport idealized torsional DOFs Statistics Scientific Benchmark
src/protocols/features/ProteinResidueConformationFeatures.fwd.hhReport residue level geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ProteinResidueConformationFeatures.hhReport idealized torsional DOFs Statistics Scientific Benchmark
src/protocols/features/ProteinResidueConformationFeaturesCreator.cc
src/protocols/features/ProteinResidueConformationFeaturesCreator.hhHeader for ProteinResidueConformationFeaturesCreator for the ProteinResidueConformationFeatures load-time factory registration scheme
src/protocols/features/ProteinRMSDFeatures.ccReport comments stored with each pose
src/protocols/features/ProteinRMSDFeatures.fwd.hhReport RMSD similarity of a protein structure against supplied reference structure
src/protocols/features/ProteinRMSDFeatures.hhReport ProteinRMSD similarity of structure against supplied reference structure
src/protocols/features/ProteinRMSDFeaturesCreator.cc
src/protocols/features/ProteinRMSDFeaturesCreator.hhHeader for ProteinRMSDFeaturesCreator for the ProteinRMSDFeatures load-time factory registration scheme
src/protocols/features/ProteinSilentReport.cc
src/protocols/features/ProteinSilentReport.fwd.hhReport pose fold tree related features
src/protocols/features/ProteinSilentReport.hhReport feature data to database
src/protocols/features/ProtocolFeatures.ccReport protocol level features to features statistics scientific benchmark
src/protocols/features/ProtocolFeatures.fwd.hhReport Orbital geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ProtocolFeatures.hhReport Orbital geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ProtocolFeaturesCreator.cc
src/protocols/features/ProtocolFeaturesCreator.hhHeader for ProtocolFeaturesCreator for the ProtocolFeatures load-time factory registration scheme
src/protocols/features/RadiusOfGyrationFeatures.ccReport the radius of gyration to features Statistics Scientific Benchmark
src/protocols/features/RadiusOfGyrationFeatures.fwd.hhReport the radius of gyration to features Statistics Scientific Benchmark
src/protocols/features/RadiusOfGyrationFeatures.hhReport the radius of gyration to features Statistics Scientific Benchmark
src/protocols/features/RadiusOfGyrationFeaturesCreator.cc
src/protocols/features/RadiusOfGyrationFeaturesCreator.hhHeader for RadiusOfGyrationFeaturesCreator for the RadiusOfGyrationFeatures load-time factory registration scheme
src/protocols/features/Report.cc
src/protocols/features/Report.fwd.hhReport pose fold tree related features
src/protocols/features/Report.hhReport feature data to database
src/protocols/features/ReportToDB.ccReport all data to a database
src/protocols/features/ReportToDB.fwd.hhReport data to sqlite database
src/protocols/features/ReportToDB.hhReport feature data to sqlite database
src/protocols/features/ReportToDBCreator.hhThis class will create instances of Mover ReportToDB for the MoverFactory
src/protocols/features/ResidueBurialFeatures.ccReport residue burial to features statistics scientific benchmark
src/protocols/features/ResidueBurialFeatures.fwd.hhReport residue level geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueBurialFeatures.hhReport residue to features Statistics Scientific Benchmark
src/protocols/features/ResidueBurialFeaturesCreator.cc
src/protocols/features/ResidueBurialFeaturesCreator.hhHeader for ResidueBurialFeaturesCreator for the ResidueBurialFeatures load-time factory registration scheme
src/protocols/features/ResidueConformationFeatures.ccReport idealized torsional DOFs Statistics Scientific Benchmark
src/protocols/features/ResidueConformationFeatures.fwd.hhReport residue level geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueConformationFeatures.hh
src/protocols/features/ResidueConformationFeaturesCreator.cc
src/protocols/features/ResidueConformationFeaturesCreator.hhHeader for ResidueConformationFeaturesCreator for the ResidueConformationFeatures load-time factory registration scheme
src/protocols/features/ResidueFeatures.ccReport residue features to features Statistics Scientific Benchmark
src/protocols/features/ResidueFeatures.fwd.hhReport residue features to features Statistics Scientific Benchmark
src/protocols/features/ResidueFeatures.hhReport residue to features Statistics Scientific Benchmark
src/protocols/features/ResidueFeaturesCreator.cc
src/protocols/features/ResidueFeaturesCreator.hhHeader for ResidueFeaturesCreator for the ResidueFeatures load-time factory registration scheme
src/protocols/features/ResidueScoresFeatures.ccReport residue scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueScoresFeatures.fwd.hhReport residue scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueScoresFeatures.hhReport residue scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueScoresFeaturesCreator.cc
src/protocols/features/ResidueScoresFeaturesCreator.hhHeader for ResidueScoresFeaturesCreator for the ResidueScoresFeatures load-time factory registration scheme
src/protocols/features/ResidueSecondaryStructureFeatures.ccReport ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueSecondaryStructureFeatures.fwd.hhReport ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueSecondaryStructureFeatures.hhReport ResidueSecondaryStructure geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueSecondaryStructureFeaturesCreator.cc
src/protocols/features/ResidueSecondaryStructureFeaturesCreator.hhHeader for ResidueSecondaryStructureFeaturesCreator for the ResidueSecondaryStructureFeatures load-time factory registration scheme
src/protocols/features/ResidueTypesFeatures.ccReport ResidueTypes to features Statistics Scientific Benchmark
src/protocols/features/ResidueTypesFeatures.fwd.hhReport ResidueTypes geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/ResidueTypesFeatures.hhReport ResidueTypes features Statistics Scientific Benchmark
src/protocols/features/ResidueTypesFeaturesCreator.cc
src/protocols/features/ResidueTypesFeaturesCreator.hhHeader for ResidueTypesFeaturesCreator for the ResidueTypesFeatures load-time factory registration scheme
src/protocols/features/RotamerBoltzmannWeightFeatures.ccReport residue burial to features statistics scientific benchmark
src/protocols/features/RotamerBoltzmannWeightFeatures.fwd.hhReport rotamer boltzmann weights to features Statistics Scientific Benchmark
src/protocols/features/RotamerBoltzmannWeightFeatures.hhReport rotamer boltzmann weights to features Statistics Scientific Benchmark
src/protocols/features/RotamerBoltzmannWeightFeaturesCreator.cc
src/protocols/features/RotamerBoltzmannWeightFeaturesCreator.hhHeader for RotamerBoltzmannWeightFeaturesCreator for the RotamerBoltzmannWeightFeatures load-time factory registration scheme
src/protocols/features/RotamerRecoveryFeatures.ccReport rotamer recover features and scores to features Statistics Scientific Benchmark
src/protocols/features/RotamerRecoveryFeatures.fwd.hhReport Rotamer Recovery features to features Statistics Scientific Benchmark
src/protocols/features/RotamerRecoveryFeatures.hhReport Rotamer Recovery Statistics Scientific Benchmark
src/protocols/features/RotamerRecoveryFeaturesCreator.cc
src/protocols/features/RotamerRecoveryFeaturesCreator.hhHeader for RotamerRecoveryFeaturesCreator for the RotamerRecoveryFeatures load-time factory registration scheme
src/protocols/features/SaltBridgeFeatures.ccReport geometric solvation energy for each polar site to a features database
src/protocols/features/SaltBridgeFeatures.fwd.hhReport geometric solvation for each polar site to features Statistics Scientific Benchmark
src/protocols/features/SaltBridgeFeatures.hhReport comments stored with each pose
src/protocols/features/SaltBridgeFeaturesCreator.cc
src/protocols/features/SaltBridgeFeaturesCreator.hhHeader for SaltBridgeFeaturesCreator for the SaltBridgeFeatures load-time factory registration scheme
src/protocols/features/ScoreTypeFeatures.ccReport protocol level features to features statistics scientific benchmark
src/protocols/features/ScoreTypeFeatures.fwd.hhStructure scores to features Statistics Scientific Benchmark
src/protocols/features/ScoreTypeFeatures.hhStructure scores to features Statistics Scientific Benchmark
src/protocols/features/ScoreTypeFeaturesCreator.cc
src/protocols/features/ScoreTypeFeaturesCreator.hhHeader for ScoreTypeFeaturesCreator for the ScoreTypeFeatures load-time factory registration scheme
src/protocols/features/StructureFeatures.cc
src/protocols/features/StructureFeatures.fwd.hhReport structure features to features Statistics Scientific Benchmark
src/protocols/features/StructureFeatures.hhReport Orbital geometry and scores to features Statistics Scientific Benchmark
src/protocols/features/StructureFeaturesCreator.cc
src/protocols/features/StructureFeaturesCreator.hhHeader for StructureFeaturesCreator for the StructureFeatures load-time factory registration scheme
src/protocols/features/StructureScoresFeatures.ccReport protocol level features to features statistics scientific benchmark
src/protocols/features/StructureScoresFeatures.fwd.hhStructure scores to features Statistics Scientific Benchmark
src/protocols/features/StructureScoresFeatures.hhStructure scores to features Statistics Scientific Benchmark
src/protocols/features/StructureScoresFeaturesCreator.cc
src/protocols/features/StructureScoresFeaturesCreator.hhHeader for StructureScoresFeaturesCreator for the StructureScoresFeatures load-time factory registration scheme
src/protocols/features/helixAssembly/HelicalFragment.cc
src/protocols/features/helixAssembly/HelicalFragment.hhSmall helper class that stores the start and end of a helix secondary structure
src/protocols/features/helixAssembly/HelixBundleFeatures.ccSearch through a pose for sets of 3 helices and generate RMSD calculations between all pairs of them
src/protocols/features/helixAssembly/HelixBundleFeatures.fwd.hh
src/protocols/features/helixAssembly/HelixBundleFeatures.hh
src/protocols/features/helixAssembly/HelixBundleFeaturesCreator.cc
src/protocols/features/helixAssembly/HelixBundleFeaturesCreator.hh
src/protocols/fibril/fibril_util.cc
src/protocols/fibril/fibril_util.hhUtility functions for handling of fibril symmetry modeling
src/protocols/fibril/SetupForFibrilMover.cc
src/protocols/fibril/SetupForFibrilMover.fwd.hh
src/protocols/fibril/SetupForFibrilMover.hh
src/protocols/filters/BasicFilterCreators.hhFilterCreators for the most basic of filters
src/protocols/filters/BasicFilters.cc
src/protocols/filters/BasicFilters.fwd.hh
src/protocols/filters/BasicFilters.hhHeader file for very simple Filter classes
src/protocols/filters/CompleteConnectionsFilter.cc
src/protocols/filters/CompleteConnectionsFilter.hh
src/protocols/filters/ContingentFilter.cc
src/protocols/filters/ContingentFilter.fwd.hh
src/protocols/filters/ContingentFilter.hhA filter that is contingent on some other mover to set its pass/fail value
src/protocols/filters/ContingentFilterCreator.hhFilterCreator for the ContingentFilter
src/protocols/filters/Filter.cc
src/protocols/filters/Filter.fwd.hh
src/protocols/filters/Filter.hhHeader file for Filter base class
src/protocols/filters/FilterCreator.cc
src/protocols/filters/FilterCreator.hhBase class for FilterCreators for the Filter load-time factory registration scheme
src/protocols/filters/FilterFactory.cc
src/protocols/filters/FilterFactory.fwd.hhForward declaration of Factory class for Filters
src/protocols/filters/FilterFactory.hh
src/protocols/filters/HeavyAtomFilter.cc
src/protocols/filters/HeavyAtomFilter.hh
src/protocols/filters/TimeFilter.cc
src/protocols/filters/TimeFilter.hh
src/protocols/filters/TimeFilterCreator.hhFilterCreator for the TimeFilter
src/protocols/fldsgn/BluePrintBDR.cc
src/protocols/fldsgn/BluePrintBDR.fwd.hhForward declaration for BluePrintBDR
src/protocols/fldsgn/BluePrintBDR.hh
src/protocols/fldsgn/BluePrintBDRCreator.hhThis class will create instances of Mover BluePrintBDR for the MoverFactory
src/protocols/fldsgn/CircularPermutation.ccPerform circularpermutation give a pose ( under development )
src/protocols/fldsgn/CircularPermutation.fwd.hhForward declaration for CircularPermutation
src/protocols/fldsgn/CircularPermutation.hh
src/protocols/fldsgn/CircularPermutationCreator.hh
src/protocols/fldsgn/NcontactsCalculator.cc
src/protocols/fldsgn/NcontactsCalculator.hhHeader file for NcontactsCalculator class
src/protocols/fldsgn/SheetConstraintsRCG.cc
src/protocols/fldsgn/SheetConstraintsRCG.fwd.hh
src/protocols/fldsgn/SheetConstraintsRCG.hh
src/protocols/fldsgn/filters/CoreDunbrackFilter.cc
src/protocols/fldsgn/filters/CoreDunbrackFilter.fwd.hh
src/protocols/fldsgn/filters/CoreDunbrackFilter.hhHeader file for CoreDunbrackFilter class
src/protocols/fldsgn/filters/CoreDunbrackFilterCreator.hhFilterCreators for the CoreDunbrackFilter
src/protocols/fldsgn/filters/FragQualFilter.cc
src/protocols/fldsgn/filters/FragQualFilter.fwd.hh
src/protocols/fldsgn/filters/FragQualFilter.hhHeader file for FragQualFilter class
src/protocols/fldsgn/filters/FragQualFilterCreator.hhFilterCreators for the FragQualFilter
src/protocols/fldsgn/filters/HelixKinkFilter.cc
src/protocols/fldsgn/filters/HelixKinkFilter.fwd.hh
src/protocols/fldsgn/filters/HelixKinkFilter.hhHeader file for HelixKinkFilter class
src/protocols/fldsgn/filters/HelixKinkFilterCreator.hhFilterCreators for the HelixKinkFilter
src/protocols/fldsgn/filters/HelixPairingFilter.cc
src/protocols/fldsgn/filters/HelixPairingFilter.fwd.hh
src/protocols/fldsgn/filters/HelixPairingFilter.hhHeader file for HelixPairingFilter class
src/protocols/fldsgn/filters/HelixPairingFilterCreator.hhFilterCreators for the HelixPairingFilter
src/protocols/fldsgn/filters/HSSTripletFilter.cc
src/protocols/fldsgn/filters/HSSTripletFilter.fwd.hh
src/protocols/fldsgn/filters/HSSTripletFilter.hhHeader file for HSSTripletFilter class
src/protocols/fldsgn/filters/HSSTripletFilterCreator.hhFilterCreators for the HSSTripletFilter
src/protocols/fldsgn/filters/InterlockingAromaFilter.cc
src/protocols/fldsgn/filters/InterlockingAromaFilter.fwd.hh
src/protocols/fldsgn/filters/InterlockingAromaFilter.hhHeader file for InterlockingAromaFilter class
src/protocols/fldsgn/filters/InterlockingAromaFilterCreator.hhFilterCreators for the InterlockingAromaFilter
src/protocols/fldsgn/filters/NcontactsFilter.cc
src/protocols/fldsgn/filters/NcontactsFilter.fwd.hh
src/protocols/fldsgn/filters/NcontactsFilter.hhHeader file for NcontactsFilter class
src/protocols/fldsgn/filters/NcontactsFilterCreator.hhFilterCreators for the NcontactsFilter
src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.cc
src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.fwd.hh
src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.hhHeader file for ParallelBetaPairingPreferenceFilter class
src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilterCreator.hhFilterCreators for the ParallelBetaPairingPreferenceFilter
src/protocols/fldsgn/filters/SecondaryStructureFilter.cc
src/protocols/fldsgn/filters/SecondaryStructureFilter.fwd.hh
src/protocols/fldsgn/filters/SecondaryStructureFilter.hhHeader file for SecondaryStructureFilter class
src/protocols/fldsgn/filters/SecondaryStructureFilterCreator.hhFilterCreators for the SecondaryStructureFilter
src/protocols/fldsgn/filters/SheetTopologyFilter.cc
src/protocols/fldsgn/filters/SheetTopologyFilter.fwd.hh
src/protocols/fldsgn/filters/SheetTopologyFilter.hhHeader file for SheetTopologyFilter class
src/protocols/fldsgn/filters/SheetTopologyFilterCreator.hhFilterCreators for the SheetTopologyFilter
src/protocols/fldsgn/potentials/AACompositionEnergy.cc
src/protocols/fldsgn/potentials/AACompositionEnergy.fwd.hh
src/protocols/fldsgn/potentials/AACompositionEnergy.hhAmino acid composition energy
src/protocols/fldsgn/potentials/AACompositionEnergyCreator.hh
src/protocols/fldsgn/potentials/SetAACompositionPotential.cc
src/protocols/fldsgn/potentials/SetAACompositionPotential.fwd.hh
src/protocols/fldsgn/potentials/SetAACompositionPotential.hh
src/protocols/fldsgn/potentials/SetAACompositionPotentialCreator.hh
src/protocols/fldsgn/potentials/SetSecStructEnergies.cc
src/protocols/fldsgn/potentials/SetSecStructEnergies.fwd.hh
src/protocols/fldsgn/potentials/SetSecStructEnergies.hhMover for setting centroid score of secondary structure through parser
src/protocols/fldsgn/potentials/SetSecStructEnergiesCreator.hh
src/protocols/fldsgn/potentials/sspot/HSPairPotential.cc
src/protocols/fldsgn/potentials/sspot/HSPairPotential.fwd.hh
src/protocols/fldsgn/potentials/sspot/HSPairPotential.hh
src/protocols/fldsgn/potentials/sspot/NatbiasHelicesSheetPotential.ccNative-biased centroid score for helices on sheets
src/protocols/fldsgn/potentials/sspot/NatbiasHelicesSheetPotential.fwd.hh
src/protocols/fldsgn/potentials/sspot/NatbiasHelicesSheetPotential.hhCentroid score for helices on sheet
src/protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.ccCalss for helix-pairing potential
src/protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.fwd.hh
src/protocols/fldsgn/potentials/sspot/NatbiasHelixPairPotential.hh
src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.ccNative biased centroid score for secondary structures
src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.fwd.hh
src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.hhNative biased centroid score for secondary structure
src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergyCreator.hhDeclaration for the class that connects NatbiasSecondaryStructureEnergy with the ScoringManager
src/protocols/fldsgn/potentials/sspot/NatbiasSheetPotential.ccHeader file of NatbiasSheetPotential
src/protocols/fldsgn/potentials/sspot/NatbiasSheetPotential.fwd.hh
src/protocols/fldsgn/potentials/sspot/NatbiasSheetPotential.hh
src/protocols/fldsgn/potentials/sspot/NatbiasStrandPairPotential.cc
src/protocols/fldsgn/potentials/sspot/NatbiasStrandPairPotential.fwd.hh
src/protocols/fldsgn/potentials/sspot/NatbiasStrandPairPotential.hhNative biased centroid score for strand pairings
src/protocols/fldsgn/potentials/sspot/SSPairPotential.cc
src/protocols/fldsgn/potentials/sspot/SSPairPotential.fwd.hh
src/protocols/fldsgn/potentials/sspot/SSPairPotential.hh
src/protocols/fldsgn/potentials/sspot/util.cc
src/protocols/fldsgn/potentials/sspot/util.hhHelper functions for SSPairPotential and HSPairPotential
src/protocols/fldsgn/topology/BB_Pos.cc
src/protocols/fldsgn/topology/BB_Pos.fwd.hh
src/protocols/fldsgn/topology/BB_Pos.hhBb_pos class header
src/protocols/fldsgn/topology/BetaAlphaBetaMotif.cc
src/protocols/fldsgn/topology/BetaAlphaBetaMotif.fwd.hh
src/protocols/fldsgn/topology/BetaAlphaBetaMotif.hh
src/protocols/fldsgn/topology/DimerPairing.cc
src/protocols/fldsgn/topology/DimerPairing.fwd.hh
src/protocols/fldsgn/topology/DimerPairing.hh
src/protocols/fldsgn/topology/HelixPairing.ccClass for helix pairings
src/protocols/fldsgn/topology/HelixPairing.fwd.hh
src/protocols/fldsgn/topology/HelixPairing.hhHeader file of HelixPairing.cc
src/protocols/fldsgn/topology/HSSTriplet.cc
src/protocols/fldsgn/topology/HSSTriplet.fwd.hh
src/protocols/fldsgn/topology/HSSTriplet.hh
src/protocols/fldsgn/topology/Sheet.cc
src/protocols/fldsgn/topology/Sheet.fwd.hh
src/protocols/fldsgn/topology/Sheet.hh
src/protocols/fldsgn/topology/SheetFoldTypeManager.cc
src/protocols/fldsgn/topology/SheetFoldTypeManager.fwd.hh
src/protocols/fldsgn/topology/SheetFoldTypeManager.hh
src/protocols/fldsgn/topology/SS_Info2.cc
src/protocols/fldsgn/topology/SS_Info2.fwd.hh
src/protocols/fldsgn/topology/SS_Info2.hh
src/protocols/fldsgn/topology/StrandPairing.cc
src/protocols/fldsgn/topology/StrandPairing.fwd.hh
src/protocols/fldsgn/topology/StrandPairing.hh
src/protocols/fldsgn/topology/util.ccUtilities for fldsgn/topology
src/protocols/fldsgn/topology/util.hh
src/protocols/flexpack/FlexPacker.cc
src/protocols/flexpack/FlexPacker.fwd.hh
src/protocols/flexpack/FlexPacker.hh
src/protocols/flexpack/OtherContextScoreFunction.cc
src/protocols/flexpack/OtherContextScoreFunction.hh
src/protocols/flexpack/annealer/FlexbbSimAnnealer.ccAnnealer for optimizing both backbone and sidechain conformations implementation
src/protocols/flexpack/annealer/FlexbbSimAnnealer.fwd.hhForward declarations and typedefs for the FlexbbSimAnnealer class
src/protocols/flexpack/annealer/FlexbbSimAnnealer.hh
src/protocols/flexpack/interaction_graph/FlexbbIGFactory.cc
src/protocols/flexpack/interaction_graph/FlexbbIGFactory.fwd.hh
src/protocols/flexpack/interaction_graph/FlexbbIGFactory.hh
src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.cc
src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.fwd.hhForward declaration of base-class FlexbbIG and associated typedefs
src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.hh
src/protocols/flexpack/interaction_graph/FlexbbSparseMatrixIndex.hhDeclaration of class for maintaining sparse matrix indices for flexbb states
src/protocols/flexpack/interaction_graph/MinimalistFlexbbInteractionGraph.ccClass implementation for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph
src/protocols/flexpack/interaction_graph/MinimalistFlexbbInteractionGraph.fwd.hhClass forward declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph
src/protocols/flexpack/interaction_graph/MinimalistFlexbbInteractionGraph.hhClass declaration for minimimalist on-the-fly RPE calculating FlexbbInteractionGraph
src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.ccClass implementation for OTF flexbb IG
src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.fwd.hh
src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.hh
src/protocols/flexpack/interaction_graph/PrecomputedFlexbbInteractionGraph.cc
src/protocols/flexpack/interaction_graph/PrecomputedFlexbbInteractionGraph.fwd.hh
src/protocols/flexpack/interaction_graph/PrecomputedFlexbbInteractionGraph.hh
src/protocols/flexpack/rotamer_set/FlexbbRotamerSet.cc
src/protocols/flexpack/rotamer_set/FlexbbRotamerSet.fwd.hh
src/protocols/flexpack/rotamer_set/FlexbbRotamerSet.hhDeclaration for a class to hold rotamers for a single backbone conformation in a flexible packing run
src/protocols/flexpack/rotamer_set/FlexbbRotamerSets.cc
src/protocols/flexpack/rotamer_set/FlexbbRotamerSets.fwd.hh
src/protocols/flexpack/rotamer_set/FlexbbRotamerSets.hhDeclaration for a class to hold a set of rotamers for a flexible packing run
src/protocols/flexpep_docking/FlexPepDockingAbInitio.cc
src/protocols/flexpep_docking/FlexPepDockingAbInitio.fwd.hh
src/protocols/flexpep_docking/FlexPepDockingAbInitio.hhLow-resolution part of docking protocol
src/protocols/flexpep_docking/FlexPepDockingFlags.ccFlags structure for FlexPepDocking protocols
src/protocols/flexpep_docking/FlexPepDockingFlags.fwd.hhFlags structure for FlexPepDocking protocols - forward declarations
src/protocols/flexpep_docking/FlexPepDockingFlags.hhFlags structure for FlexPepDocking protocols
src/protocols/flexpep_docking/FlexPepDockingLowRes.cc
src/protocols/flexpep_docking/FlexPepDockingLowRes.fwd.hh
src/protocols/flexpep_docking/FlexPepDockingLowRes.hhLow-resolution part of docking protocol
src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.ccMetrics calculations specific for FlexPepDock (at least for now)
src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.fwd.hh
src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.hhMetrics calculations specific for FlexPepDock (at least for now)
src/protocols/flexpep_docking/FlexPepDockingProtocol.ccProtocol for docking flexible peptides onto globular proteins
src/protocols/flexpep_docking/FlexPepDockingProtocol.hhProtocol for docking flexible peptides onto globular proteins
src/protocols/flexpep_docking/FlexPepDockingProtocolCreator.hh
src/protocols/flxbb/DesignTask.cc
src/protocols/flxbb/DesignTask.fwd.hh
src/protocols/flxbb/DesignTask.hh
src/protocols/flxbb/FilterStructs.cc
src/protocols/flxbb/FilterStructs.fwd.hh
src/protocols/flxbb/FilterStructs.hhFilter structures
src/protocols/flxbb/FlxbbDesign.ccPerform cycles of design and relax with filter
src/protocols/flxbb/FlxbbDesign.fwd.hhPerform cycles of design and relax with filter
src/protocols/flxbb/FlxbbDesign.hhPerform cycles of design and relax with filter
src/protocols/flxbb/FlxbbDesign_main.cc
src/protocols/flxbb/FlxbbDesign_main.hh
src/protocols/flxbb/FlxbbDesignCreator.hh
src/protocols/flxbb/InterlockAroma.ccPlace interlocking aromatic residues
src/protocols/flxbb/InterlockAroma.fwd.hh
src/protocols/flxbb/InterlockAroma.hhPerform cycles of design and relax with filter
src/protocols/flxbb/InterlockAromaCreator.hhThis class will create instances of Mover InterlockAroma for the MoverFactory
src/protocols/flxbb/LayerDesignOperation.ccDesign residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA
src/protocols/flxbb/LayerDesignOperation.fwd.hh
src/protocols/flxbb/LayerDesignOperation.hhDesign residues with selected amino acids depending on the enviroment: layer. The layer of each residue is assigned as core, boundary, or surface, which are defined by accessible surface of mainchain + CB. If resfile is read before calling this operation, this operation is not applied for the residues defined by PIKAA
src/protocols/flxbb/LayerDesignOperationCreator.hh
src/protocols/flxbb/utility.cc
src/protocols/flxbb/utility.hh
src/protocols/forge/build/Bridge.ccConnect two contiguous but disjoint sections of a Pose into one continuous section
src/protocols/forge/build/Bridge.fwd.hhForward declaration for Bridge
src/protocols/forge/build/Bridge.hhConnect two contiguous but disjoint sections of a Pose into one continuous section
src/protocols/forge/build/BuildInstruction.cc
src/protocols/forge/build/BuildInstruction.fwd.hhForward declaration for BuildInstruction
src/protocols/forge/build/BuildInstruction.hhTracks modifications to be made and is capable of residue length changes on a Pose
src/protocols/forge/build/BuildManager.cc
src/protocols/forge/build/BuildManager.fwd.hhForward declaration for BuildManager
src/protocols/forge/build/BuildManager.hhContainer for managing BuildInstructions
src/protocols/forge/build/ConnectRight.ccInstruction to connect one Pose onto the right side of another
src/protocols/forge/build/ConnectRight.fwd.hhForward declaration for ConnectRight
src/protocols/forge/build/ConnectRight.hhInstruction to connect one Pose onto the right side of another
src/protocols/forge/build/GrowLeft.ccInstruction to create an n-side extension
src/protocols/forge/build/GrowLeft.fwd.hhForward declaration for GrowLeft
src/protocols/forge/build/GrowLeft.hhInstruction to create an n-side extension
src/protocols/forge/build/GrowRight.ccInstruction to create a c-side extension
src/protocols/forge/build/GrowRight.fwd.hhForward declaration for GrowRight
src/protocols/forge/build/GrowRight.hhInstruction to create a c-side extension
src/protocols/forge/build/Interval.fwd.hhForward declaration for Interval
src/protocols/forge/build/Interval.hh
src/protocols/forge/build/RelativeConnectRight.ccVersion of ConnectRight instruction that depends upon results from another BuildInstruction
src/protocols/forge/build/RelativeConnectRight.fwd.hhForward declaration for RelativeConnectRight
src/protocols/forge/build/RelativeConnectRight.hhVersion of ConnectRight instruction that depends upon results from another BuildInstruction
src/protocols/forge/build/RelativeSequencePosition.fwd.hhForward declaration for RelativeSequencePosition
src/protocols/forge/build/RelativeSequencePosition.hhFunction objects to compute relative positions for RelativeConnectRight
src/protocols/forge/build/SegmentInsert.ccInsert an external segment flanked by new regions
src/protocols/forge/build/SegmentInsert.fwd.hhForward declaration for SegmentInsert
src/protocols/forge/build/SegmentInsert.hhInsert an external segment flanked by new regions
src/protocols/forge/build/SegmentRebuild.ccInstruction to rebuild a segment
src/protocols/forge/build/SegmentRebuild.fwd.hhForward declaration for SegmentRebuild
src/protocols/forge/build/SegmentRebuild.hhInstruction to rebuild a segment
src/protocols/forge/build/SegmentSwap.ccInstruction to swap a segment with an external segment
src/protocols/forge/build/SegmentSwap.fwd.hhForward declaration for SegmentSwap
src/protocols/forge/build/SegmentSwap.hhInstruction to swap a segment with an external segment
src/protocols/forge/components/BDR.cc
src/protocols/forge/components/BDR.fwd.hhForward declaration for BDR
src/protocols/forge/components/BDR.hh
src/protocols/forge/components/BDRSegmentInfo.fwd.hhForward declaration for BDRSegmentInfo
src/protocols/forge/components/BDRSegmentInfo.hh
src/protocols/forge/components/VarLengthBuild.ccComponent that performs a simplified version of a protocol for variable length remodeling of protein backbone segments
src/protocols/forge/components/VarLengthBuild.fwd.hhForward declaration for protocols::forge::components::VarLengthBuild
src/protocols/forge/components/VarLengthBuild.hh
src/protocols/forge/constraints/ConstraintFileRCG.cc
src/protocols/forge/constraints/ConstraintFileRCG.fwd.hh
src/protocols/forge/constraints/ConstraintFileRCG.hh
src/protocols/forge/constraints/InverseRotamersRCG.cc
src/protocols/forge/constraints/InverseRotamersRCG.fwd.hh
src/protocols/forge/constraints/InverseRotamersRCG.hh
src/protocols/forge/constraints/NtoC_RCG.cc
src/protocols/forge/constraints/NtoC_RCG.fwd.hh
src/protocols/forge/constraints/NtoC_RCG.hh
src/protocols/forge/methods/chainbreak_eval.ccMethods for chainbreak evaluation
src/protocols/forge/methods/chainbreak_eval.hhMethods for chainbreak evaluation
src/protocols/forge/methods/fold_tree_functions.ccMethods for manipulating FoldTrees
src/protocols/forge/methods/fold_tree_functions.hhMethods for manipulating FoldTrees
src/protocols/forge/methods/fragment_functions.ccMethods for manipulating fragments
src/protocols/forge/methods/fragment_functions.hhMethods for manipulating fragments
src/protocols/forge/methods/pose_mod.ccMethods for Pose modifications
src/protocols/forge/methods/pose_mod.hhMethods for Pose modifications
src/protocols/forge/methods/util.ccMiscellaneous utility functions for forge
src/protocols/forge/methods/util.hhMiscellaneous utility functions for forge
src/protocols/forge/remodel/RemodelAccumulator.cc
src/protocols/forge/remodel/RemodelAccumulator.hh
src/protocols/forge/remodel/RemodelConstraintGenerator.cc
src/protocols/forge/remodel/RemodelConstraintGenerator.fwd.hh
src/protocols/forge/remodel/RemodelConstraintGenerator.hhAbstract base class that generates constraints during forge loop remodelling
src/protocols/forge/remodel/RemodelData.cc
src/protocols/forge/remodel/RemodelData.hh
src/protocols/forge/remodel/RemodelDesignMover.cc
src/protocols/forge/remodel/RemodelDesignMover.hh
src/protocols/forge/remodel/RemodelEnzdesCstModule.cc
src/protocols/forge/remodel/RemodelEnzdesCstModule.fwd.hh
src/protocols/forge/remodel/RemodelEnzdesCstModule.hhThis file handles merging constraint defined by enzdes type cstfile
src/protocols/forge/remodel/RemodelLoopMover.ccLoop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++
src/protocols/forge/remodel/RemodelLoopMover.fwd.hhForward declaration for RemodelLoopMover
src/protocols/forge/remodel/RemodelLoopMover.hhLoop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++
src/protocols/forge/remodel/RemodelLoopMoverCreator.hhThis class will create instances of Mover RemodelLoopMover for the MoverFactory
src/protocols/forge/remodel/RemodelMover.cc
src/protocols/forge/remodel/RemodelMover.fwd.hh
src/protocols/forge/remodel/RemodelMover.hh
src/protocols/forge/remodel/RemodelMoverCreator.hh
src/protocols/forge/remodel/RemodelRotamerLinks.cc
src/protocols/forge/remodel/RemodelRotamerLinks.fwd.hh
src/protocols/forge/remodel/RemodelRotamerLinks.hhWhen operated on a PackerTask, adds RotamerLinks to it that will
src/protocols/forge/remodel/RemodelRotamerLinksCreator.hh
src/protocols/forge/remodel/RemodelWorkingSet.cc
src/protocols/forge/remodel/RemodelWorkingSet.hh
src/protocols/forge/remodel/ResidueVicinityRCG.cc
src/protocols/forge/remodel/ResidueVicinityRCG.hh
src/protocols/frag_picker/BestTotalScoreSelector.cc
src/protocols/frag_picker/BestTotalScoreSelector.fwd.hh
src/protocols/frag_picker/BestTotalScoreSelector.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/BoundedCollector.fwd.hh
src/protocols/frag_picker/BoundedCollector.hh
src/protocols/frag_picker/BoundedPriorityQueue.hh
src/protocols/frag_picker/CandidatesCollector.fwd.hhForward declaration for CandidatesCollector
src/protocols/frag_picker/CandidatesCollector.hhPure virtual base class for a container holding fragment candidates
src/protocols/frag_picker/CommonFragmentComparators.fwd.hhFew ways to compare fragment candidates (forward definitions)
src/protocols/frag_picker/CommonFragmentComparators.hhFew ways to compare fragment candidates
src/protocols/frag_picker/CompositeFragmentSelector.ccSelector that picks best fragments based on their total score
src/protocols/frag_picker/CompositeFragmentSelector.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/Contact.fwd.hh
src/protocols/frag_picker/Contact.hhA contact
src/protocols/frag_picker/ContactCounts.fwd.hh
src/protocols/frag_picker/ContactCounts.hhContact counts
src/protocols/frag_picker/ContactTypes.ccFragment picker contact types
src/protocols/frag_picker/ContactTypes.hhFragment picker type declarations
src/protocols/frag_picker/CS2ndShift.cc
src/protocols/frag_picker/CS2ndShift.hh
src/protocols/frag_picker/CSTalosIO.cc
src/protocols/frag_picker/CSTalosIO.hhClass that converts Talos object into secondary shifts list
src/protocols/frag_picker/CustomScoreSelector.cc
src/protocols/frag_picker/CustomScoreSelector.fwd.hh
src/protocols/frag_picker/CustomScoreSelector.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/DiversifyCrmsdByClustering.cc
src/protocols/frag_picker/DiversifyCrmsdByClustering.hhSelector that picks fragments diversified by crmsd (by means of hierarchical clustering)
src/protocols/frag_picker/DiversifyCrmsdSelector.cc
src/protocols/frag_picker/DiversifyCrmsdSelector.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/DiversifyDihedralsSelector.cc
src/protocols/frag_picker/DiversifyDihedralsSelector.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/Faraggi_SA.ccFaraggi maximum SA values from Faraggi et al. Proteins 2008
src/protocols/frag_picker/Faraggi_SA.hhFaraggi maximum SA values from Faraggi et al. Proteins 2008
src/protocols/frag_picker/FragmentCandidate.cc
src/protocols/frag_picker/FragmentCandidate.fwd.hh
src/protocols/frag_picker/FragmentCandidate.hhSomething that might become a fragment if its scores will be good enough
src/protocols/frag_picker/FragmentComparatorBase.fwd.hh
src/protocols/frag_picker/FragmentComparatorBase.hhDefines a base class for all fragment comparators
src/protocols/frag_picker/FragmentPicker.ccFragment picker - the core part of picking machinery
src/protocols/frag_picker/FragmentPicker.fwd.hhFragment picker - forward declaration
src/protocols/frag_picker/FragmentPicker.hhFragment picker - the core part of picking machinery
src/protocols/frag_picker/FragmentSelectingRule.fwd.hh
src/protocols/frag_picker/FragmentSelectingRule.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/GrabAllCollector.hh
src/protocols/frag_picker/JCouplingIO.cc
src/protocols/frag_picker/JCouplingIO.hh
src/protocols/frag_picker/LAMBEGO_IO.cc
src/protocols/frag_picker/LAMBEGO_IO.hhReader for a probability distribution over A,B,E,G,O torsion bins
src/protocols/frag_picker/LazySortedVector1.hh
src/protocols/frag_picker/PdbIdChunkFilter.cc
src/protocols/frag_picker/PdbIdChunkFilter.fwd.hh
src/protocols/frag_picker/PdbIdChunkFilter.hh
src/protocols/frag_picker/PhiPsiTalosIO.cc
src/protocols/frag_picker/PhiPsiTalosIO.hhClass that reads and writes Phi-Psi in TALOS format
src/protocols/frag_picker/SidechainContactDistCutoff.ccDefines sidechain contact distance cutoffs
src/protocols/frag_picker/SidechainContactDistCutoff.fwd.hh
src/protocols/frag_picker/SidechainContactDistCutoff.hhDefines sidechain contact distance cutoffs
src/protocols/frag_picker/TorsionBinIO.cc
src/protocols/frag_picker/TorsionBinIO.hhReader for a probability distribution over A,B,E,G,O torsion bins
src/protocols/frag_picker/VallChunk.ccContiguous chunk of residues taken from a vall
src/protocols/frag_picker/VallChunk.fwd.hhForward declaration for VallChunk
src/protocols/frag_picker/VallChunk.hhContiguous chunk of residues taken from a vall
src/protocols/frag_picker/VallChunkFilter.fwd.hhForward declaration for VallChunkFilter
src/protocols/frag_picker/VallChunkFilter.hhDefines two basic chunk filters based on pdb id
src/protocols/frag_picker/VallProvider.ccReads a vall library and serves the data in chunks
src/protocols/frag_picker/VallProvider.fwd.hhForward declaration for VallProvider
src/protocols/frag_picker/VallProvider.hhReads a vall library and serves the data in chunks
src/protocols/frag_picker/VallResidue.ccClass for managing a line of the Vall fragment library
src/protocols/frag_picker/VallResidue.fwd.hhForward declaration for core::fragment::picking::vall:VallResidue
src/protocols/frag_picker/VallResidue.hhClass for managing a line of the Vall fragment library
src/protocols/frag_picker/nonlocal/NonlocalFrags.cc
src/protocols/frag_picker/nonlocal/NonlocalFrags.fwd.hh
src/protocols/frag_picker/nonlocal/NonlocalFrags.hh
src/protocols/frag_picker/nonlocal/NonlocalFragsMain.cc
src/protocols/frag_picker/nonlocal/NonlocalFragsMain.hh
src/protocols/frag_picker/nonlocal/NonlocalPair.fwd.hhForward declaration for NonlocalPair
src/protocols/frag_picker/nonlocal/NonlocalPair.hhNonlocal fragment pair
src/protocols/frag_picker/quota/ABEGO_SS_Config.cc
src/protocols/frag_picker/quota/ABEGO_SS_Config.hhReads a config file for quota selector
src/protocols/frag_picker/quota/ABEGO_SS_Map.ccMap ABEGO vs. SS combinations
src/protocols/frag_picker/quota/ABEGO_SS_Map.fwd.hh
src/protocols/frag_picker/quota/ABEGO_SS_Map.hhClass for a quota pool based on secondary structure prediction and ABEGO torsion bin classification
src/protocols/frag_picker/quota/ABEGO_SS_Pool.cc
src/protocols/frag_picker/quota/ABEGO_SS_Pool.fwd.hhClass for a quota pool based on secondary structure prediction and ABEGO torsion bin classification
src/protocols/frag_picker/quota/ABEGO_SS_Pool.hhQuota selector based on difefrent secondary structure predicitons
src/protocols/frag_picker/quota/QuotaCollector.cc
src/protocols/frag_picker/quota/QuotaCollector.fwd.hhForward declaration for QuotaCollector
src/protocols/frag_picker/quota/QuotaCollector.hhPure virtual base class for a container holding fragment candidates
src/protocols/frag_picker/quota/QuotaConfig.cc
src/protocols/frag_picker/quota/QuotaConfig.hhReads a config file for quota selector
src/protocols/frag_picker/quota/QuotaPool.fwd.hhBase class for a quota pool
src/protocols/frag_picker/quota/QuotaPool.hhSingle pool used by quota
src/protocols/frag_picker/quota/QuotaSelector.cc
src/protocols/frag_picker/quota/QuotaSelector.fwd.hh
src/protocols/frag_picker/quota/QuotaSelector.hhSelector that picks best fragments based on their total score
src/protocols/frag_picker/quota/SecondaryStructurePool.cc
src/protocols/frag_picker/quota/SecondaryStructurePool.fwd.hhClass for a quota pool based on secondary structure prediction
src/protocols/frag_picker/quota/SecondaryStructurePool.hhQuota selector based on difefrent secondary structure predicitons
src/protocols/frag_picker/quota/TorsionBinPool.cc
src/protocols/frag_picker/quota/TorsionBinPool.hhQuota selector based on torsion bin prediciton
src/protocols/frag_picker/scores/ABEGO_SS_Score.ccScores a fragment by secondary structure similarity
src/protocols/frag_picker/scores/ABEGO_SS_Score.hhScores a fragment by secondary structure similarity
src/protocols/frag_picker/scores/AdaptiveScoreHistogram.cc
src/protocols/frag_picker/scores/AdaptiveScoreHistogram.fwd.hhAdaptiveScoreHistogram forward declaration
src/protocols/frag_picker/scores/AdaptiveScoreHistogram.hhA very basic histogram to keep statistics of scores
src/protocols/frag_picker/scores/AmbigCSScore.ccObject that scores a fragment by target-observed/vall-predicted chemical shift distances
src/protocols/frag_picker/scores/AmbigCSScore.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/AtomBasedConstraintsScore.cc
src/protocols/frag_picker/scores/AtomBasedConstraintsScore.fwd.hhAtomBasedConstraintsScore forward declaration
src/protocols/frag_picker/scores/AtomBasedConstraintsScore.hh
src/protocols/frag_picker/scores/AtomPairConstraintsScore.cc
src/protocols/frag_picker/scores/AtomPairConstraintsScore.fwd.hh
src/protocols/frag_picker/scores/AtomPairConstraintsScore.hh
src/protocols/frag_picker/scores/BFactor.ccBase class for fragment scoring
src/protocols/frag_picker/scores/BFactor.hhBase class for fragment scoring
src/protocols/frag_picker/scores/CachingScoringMethod.hhAdds cashing functionality to a FragmentScoringMethod object
src/protocols/frag_picker/scores/ConstScore.hhScore that adds a constant (so basically it does nothing!)
src/protocols/frag_picker/scores/CSScore.ccObject that scores a fragment by target-observed/vall-predicted chemical shift distances
src/protocols/frag_picker/scores/CSScore.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/DihedralConstraintsScore.ccCalculates a score based on how close are dihdral angles in a Vall chunk to their target values
src/protocols/frag_picker/scores/DihedralConstraintsScore.fwd.hhDihedralConstraintsScore forward declaration
src/protocols/frag_picker/scores/DihedralConstraintsScore.hh
src/protocols/frag_picker/scores/DisulfideDistance.cc
src/protocols/frag_picker/scores/DisulfideDistance.hh
src/protocols/frag_picker/scores/DisulfideIdentity.ccBase class for fragment scoring
src/protocols/frag_picker/scores/DisulfideIdentity.hhBase class for fragment scoring
src/protocols/frag_picker/scores/FourAtomsConstraintData.cc
src/protocols/frag_picker/scores/FourAtomsConstraintData.fwd.hh
src/protocols/frag_picker/scores/FourAtomsConstraintData.hhHolder for data necessary to create a single constraint based on four atoms
src/protocols/frag_picker/scores/fragment_scoring_utilities.cc
src/protocols/frag_picker/scores/fragment_scoring_utilities.hhFunctions and data types common for fragment scoring
src/protocols/frag_picker/scores/FragmentAllAtomCrmsd.ccObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/FragmentAllAtomCrmsd.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/FragmentCrmsd.ccScores fragments by disulfide-linke Calpha distances
src/protocols/frag_picker/scores/FragmentCrmsd.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/FragmentCrmsdResDepth.ccObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/FragmentCrmsdResDepth.hhObject that scores a fragment by its crmsd and residue depth to the native
src/protocols/frag_picker/scores/FragmentDME.ccObject that scores a fragment by its Distance Matrix Error (DME) to the native
src/protocols/frag_picker/scores/FragmentDME.hhObject that scores a fragment by its Distance Matrix Error (DME) to the native
src/protocols/frag_picker/scores/FragmentScoreManager.cc
src/protocols/frag_picker/scores/FragmentScoreManager.fwd.hhFragmentScoreManager forward declaration
src/protocols/frag_picker/scores/FragmentScoreManager.hhFragmentScoreManager forward declaration
src/protocols/frag_picker/scores/FragmentScoreMap.fwd.hhFragmentScoreMap forward declaration
src/protocols/frag_picker/scores/FragmentScoreMap.hh
src/protocols/frag_picker/scores/FragmentScoringMethod.fwd.hh
src/protocols/frag_picker/scores/FragmentScoringMethod.hhFragmentScoringMethod forward declaration
src/protocols/frag_picker/scores/GunnCost.cc
src/protocols/frag_picker/scores/GunnCost.hh
src/protocols/frag_picker/scores/GunnCostScore.ccObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/GunnCostScore.hhObject that scores a fragment by Gunn cost function (how it fits to the local structure)
src/protocols/frag_picker/scores/HydrophobicityProfileSimilarity.ccBase class for fragment scoring
src/protocols/frag_picker/scores/HydrophobicityProfileSimilarity.hhObject that scores a fragment by hydrophobicity
src/protocols/frag_picker/scores/HydrophobicitySimilarity.ccBase class for fragment scoring
src/protocols/frag_picker/scores/HydrophobicitySimilarity.hhObject that scores a fragment by hydrophobicity
src/protocols/frag_picker/scores/InterbondAngleScore.cc
src/protocols/frag_picker/scores/InterbondAngleScore.fwd.hh
src/protocols/frag_picker/scores/InterbondAngleScore.hh
src/protocols/frag_picker/scores/JCoupling.cc
src/protocols/frag_picker/scores/JCoupling.hh
src/protocols/frag_picker/scores/LAMBEGO_Similarity.cc
src/protocols/frag_picker/scores/LAMBEGO_Similarity.hh
src/protocols/frag_picker/scores/MidPhiOut.cc
src/protocols/frag_picker/scores/MidPhiOut.hhScores fragments by disulfide-linke Calpha distances
src/protocols/frag_picker/scores/MidPsiOut.cc
src/protocols/frag_picker/scores/MidPsiOut.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/PartialSecondarySimilarity.ccScores a fragment by secondary structure similarity but throws out the worst 20% of the residue matches
src/protocols/frag_picker/scores/PartialSecondarySimilarity.hh
src/protocols/frag_picker/scores/PCS_FragDistance.cc
src/protocols/frag_picker/scores/PCS_FragDistance.hh
src/protocols/frag_picker/scores/Phi.ccBase class for fragment scoring
src/protocols/frag_picker/scores/Phi.hhObject that scores a fragment by predicted Phi torsions
src/protocols/frag_picker/scores/PhiPsiRmsd.cc
src/protocols/frag_picker/scores/PhiPsiRmsd.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/PhiPsiSquareWell.cc
src/protocols/frag_picker/scores/PhiPsiSquareWell.hh
src/protocols/frag_picker/scores/ProfileScore.ccScores a fragment by an amino acid sequence identity
src/protocols/frag_picker/scores/ProfileScore.fwd.hh
src/protocols/frag_picker/scores/ProfileScore.hhFragmentScoringMethod forward declaration
src/protocols/frag_picker/scores/ProfileScoreBlosum62.cc
src/protocols/frag_picker/scores/ProfileScoreBlosum62.hh
src/protocols/frag_picker/scores/ProfileScoreDistWeight.cc
src/protocols/frag_picker/scores/ProfileScoreDistWeight.hh
src/protocols/frag_picker/scores/ProfileScoreL1.cc
src/protocols/frag_picker/scores/ProfileScoreL1.hh
src/protocols/frag_picker/scores/ProfileScoreStructL1.ccScores a fragment using structure based profiles
src/protocols/frag_picker/scores/ProfileScoreStructL1.hhScores a fragment by L1 structure based profile score
src/protocols/frag_picker/scores/ProfileScoreSubMatrix.ccScores a fragment by substitution matrix (e.g. Blosum62) profile score
src/protocols/frag_picker/scores/ProfileScoreSubMatrix.hhScores a fragment by substitution matrix (e.g. Blosum62) profile score
src/protocols/frag_picker/scores/ProlinePhiScore.cc
src/protocols/frag_picker/scores/ProlinePhiScore.hhBase class for fragment scoring
src/protocols/frag_picker/scores/Psi.ccBase class for fragment scoring
src/protocols/frag_picker/scores/Psi.hhObject that scores a fragment by predicted Psi torsions
src/protocols/frag_picker/scores/PValuedFragmentScoreManager.cc
src/protocols/frag_picker/scores/PValuedFragmentScoreManager.hhScore manager that stores statistics of all scores. This allows estimate p-value for a score
src/protocols/frag_picker/scores/RamaScore.cc
src/protocols/frag_picker/scores/RamaScore.hhBase class for fragment scoring
src/protocols/frag_picker/scores/RDCScore.ccObject that scores a fragment by its RDC
src/protocols/frag_picker/scores/RDCScore.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/RDCScore_Gront.cc
src/protocols/frag_picker/scores/RDCScore_Gront.fwd.hh
src/protocols/frag_picker/scores/RDCScore_Gront.hh
src/protocols/frag_picker/scores/ScoreEValuator.ccScores a fragment by an amino acid sequence identity
src/protocols/frag_picker/scores/ScoreEValuator.hhObject that scores a fragment by its crmsd to the native
src/protocols/frag_picker/scores/SecondaryIdentity.ccScores a fragment by an amino acid sequence identity
src/protocols/frag_picker/scores/SecondaryIdentity.hhScores a fragment by an amino acid sequence identity
src/protocols/frag_picker/scores/SecondarySimilarity.ccScores a fragment by secondary structure similarity
src/protocols/frag_picker/scores/SecondarySimilarity.hhScores a fragment by secondary structure similarity
src/protocols/frag_picker/scores/SequenceIdentity.ccBase class for fragment scoring
src/protocols/frag_picker/scores/SequenceIdentity.hhBase class for fragment scoring
src/protocols/frag_picker/scores/SolventAccessibility.ccBase class for fragment scoring
src/protocols/frag_picker/scores/SolventAccessibility.hhObject that scores a fragment by predicted solvent accessibility
src/protocols/frag_picker/scores/TalosSSSimilarity.ccScores a fragment by secondary structure similarity
src/protocols/frag_picker/scores/TalosSSSimilarity.hhScores a fragment by secondary structure similarity
src/protocols/frag_picker/scores/TorsionBinSimilarity.cc
src/protocols/frag_picker/scores/TorsionBinSimilarity.hh
src/protocols/frags/heap.cc
src/protocols/frags/heap.hh
src/protocols/frags/RMSVallData.hh
src/protocols/frags/TorsionFragment.cc
src/protocols/frags/TorsionFragment.fwd.hh
src/protocols/frags/TorsionFragment.hh
src/protocols/frags/VallData.cc
src/protocols/frags/VallData.fwd.hh
src/protocols/frags/VallData.hh
src/protocols/genetic_algorithm/Entity.cc
src/protocols/genetic_algorithm/Entity.fwd.hh
src/protocols/genetic_algorithm/Entity.hhUnit employed/optimized by GeneticAlgorithm
src/protocols/genetic_algorithm/EntityRandomizer.cc
src/protocols/genetic_algorithm/EntityRandomizer.hhControls the alteration of the traits that define Entity
src/protocols/genetic_algorithm/FitnessFunction.hhDetermines the fitness of Entity for GeneticAlgorithm
src/protocols/genetic_algorithm/GeneticAlgorithm.cc
src/protocols/genetic_algorithm/GeneticAlgorithm.fwd.hh
src/protocols/genetic_algorithm/GeneticAlgorithm.hhTemplate class for genetic algorithm protocols
src/protocols/hotspot_hashing/HotspotStub.cc
src/protocols/hotspot_hashing/HotspotStub.fwd.hh
src/protocols/hotspot_hashing/HotspotStub.hh
src/protocols/hotspot_hashing/HotspotStubSet.cc
src/protocols/hotspot_hashing/HotspotStubSet.fwd.hh
src/protocols/hotspot_hashing/HotspotStubSet.hh
src/protocols/idealize/idealize.cc
src/protocols/idealize/idealize.hhProtocols for idealizing a Pose
src/protocols/idealize/IdealizeMover.cc
src/protocols/idealize/IdealizeMover.fwd.hhProtocols for idealizing a Pose
src/protocols/idealize/IdealizeMover.hhProtocols for idealizing a Pose
src/protocols/idealize/IdealizeMoverCreator.hh
src/protocols/init/init.ccDeclare WidgetRegistrators as static (global) variables in this .cc file so that at load time, they will be initialized, and the Creator classes they register will be handed to the appropriate WidgetFactory
src/protocols/init/init.hhInitialization function to ensure all load-time factory registration occurs for classes that live in the protocols library. protocols::init::init::init() calls core::init(), and protocols::init::init() call protocols::init::init::init()
src/protocols/jd2/AtomTreeDiffJobInputter.cc
src/protocols/jd2/AtomTreeDiffJobInputter.fwd.hh
src/protocols/jd2/AtomTreeDiffJobInputter.hhHeader file for AtomTreeDiffJobInputter class
src/protocols/jd2/AtomTreeDiffJobInputterCreator.hh
src/protocols/jd2/AtomTreeDiffJobOutputter.ccAtomTreeDiffJobOutputter
src/protocols/jd2/AtomTreeDiffJobOutputter.fwd.hhHeader file for AtomTreeDiffJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/AtomTreeDiffJobOutputter.hhHeader file for AtomTreeDiffJobOutputter class
src/protocols/jd2/AtomTreeDiffJobOutputterCreator.hh
src/protocols/jd2/BatchJobInputter.cc
src/protocols/jd2/BatchJobInputter.fwd.hh
src/protocols/jd2/BatchJobInputter.hhHeader file for BatchJobInputter class
src/protocols/jd2/BOINCJobDistributor.ccImplementation of BOINCJobDistributor
src/protocols/jd2/BOINCJobDistributor.hhImplementation of BOINCJobDistributor
src/protocols/jd2/DockDesignParser.ccAugust 2008 job distributor as planned at RosettaCon08 - Interface base class Parser
src/protocols/jd2/DockDesignParser.hhHeader file for Parser class, part of August 2008 job distributor
src/protocols/jd2/FileJobOutputter.ccAugust 2008 job distributor as planned at RosettaCon08 - FileJobOutputter
src/protocols/jd2/FileJobOutputter.fwd.hhHeader file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/FileJobOutputter.hhHeader file for FileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/FileSystemJobDistributor.ccAugust 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor
src/protocols/jd2/FileSystemJobDistributor.fwd.hhAugust 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor
src/protocols/jd2/FileSystemJobDistributor.hhAugust 2008 job distributor as planned at RosettaCon08 - Simplest class FileSystemJobDistributor
src/protocols/jd2/InnerJob.cc
src/protocols/jd2/InnerJob.fwd.hhHeader file for InnerJob class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/InnerJob.hhHeader file for Job classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh)
src/protocols/jd2/InnerMultiThreadingJob.cc
src/protocols/jd2/InnerMultiThreadingJob.fwd.hhHeader file for Job classes, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/InnerMultiThreadingJob.hh
src/protocols/jd2/Job.ccAugust 2008 job distributor as planned at RosettaCon08 - Job classes
src/protocols/jd2/Job.fwd.hhHeader file for Job classes, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/Job.hhHeader file for ThreadingJob classes, part of August 2008 job distributor as planned at RosettaCon08. This file is responsible for three ideas: "inner" jobs, "outer" jobs (with which the job distributor works) and job container (currently just typdefed in the .fwd.hh)
src/protocols/jd2/JobDistributor.ccAugust 2008 job distributor as planned at RosettaCon08 - Base class
src/protocols/jd2/JobDistributor.fwd.hhAugust 2008 job distributor as planned at RosettaCon08 - Base class
src/protocols/jd2/JobDistributor.hh
src/protocols/jd2/JobDistributorFactory.cc
src/protocols/jd2/JobDistributorFactory.fwd.hh
src/protocols/jd2/JobDistributorFactory.hh
src/protocols/jd2/JobInputter.ccAugust 2008 job distributor as planned at RosettaCon08 - Interface base class JobInputter
src/protocols/jd2/JobInputter.fwd.hhHeader file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/JobInputter.hhHeader file for JobInputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/JobInputterCreator.cc
src/protocols/jd2/JobInputterCreator.hhBase class for JobInputterCreators for the JobInputter load-time factory registration scheme
src/protocols/jd2/JobInputterFactory.ccJobInputterCreator base
src/protocols/jd2/JobInputterFactory.fwd.hhJobInputterFactory forward header
src/protocols/jd2/JobInputterFactory.hhJobInputterFactory
src/protocols/jd2/JobOutputter.ccAugust 2008 job distributor as planned at RosettaCon08 - Base class JobOutputter
src/protocols/jd2/JobOutputter.fwd.hhHeader file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/JobOutputter.hhHeader file for JobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/JobOutputterCreator.cc
src/protocols/jd2/JobOutputterCreator.hhBase class for JobOutputterCreators for the JobOutputter load-time factory registration scheme
src/protocols/jd2/JobOutputterFactory.ccJobOutputterCreator base
src/protocols/jd2/JobOutputterFactory.fwd.hhJobOutputterFactory forward header
src/protocols/jd2/JobOutputterFactory.hhJobOutputterFactory
src/protocols/jd2/LazySilentFileJobInputter.cc
src/protocols/jd2/LazySilentFileJobInputter.fwd.hh
src/protocols/jd2/LazySilentFileJobInputter.hh
src/protocols/jd2/LazySilentFileJobInputterCreator.hh
src/protocols/jd2/MpiFileBuffer.cc
src/protocols/jd2/MpiFileBuffer.fwd.hh
src/protocols/jd2/MpiFileBuffer.hhHeader file for MPISilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08 this outputter will send silentstructs via MPI to dedicated node that will collect all structures
src/protocols/jd2/MPIFileBufJobDistributor.ccImplementation of MPIFileBufJobDistributor
src/protocols/jd2/MPIFileBufJobDistributor.fwd.hh
src/protocols/jd2/MPIFileBufJobDistributor.hh
src/protocols/jd2/MPIMultiCommJobDistributor.ccImplementation of MPIMultiCommJobDistributor
src/protocols/jd2/MPIMultiCommJobDistributor.fwd.hh
src/protocols/jd2/MPIMultiCommJobDistributor.hh
src/protocols/jd2/MPIWorkPartitionJobDistributor.ccImplementation of MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user
src/protocols/jd2/MPIWorkPartitionJobDistributor.fwd.hhForward header for MPIWorkPartitonJobDistributor
src/protocols/jd2/MPIWorkPartitionJobDistributor.hhHeader for MPIWorkPartitionJobDistributor - intended for MPI jobs on small numbers of nodes where the load can be balanced equally by the user
src/protocols/jd2/MPIWorkPoolJobDistributor.ccImplementation of MPIWorkPoolJobDistributor
src/protocols/jd2/MPIWorkPoolJobDistributor.fwd.hhForward header for MPIWorkPoolJobDistributor
src/protocols/jd2/MPIWorkPoolJobDistributor.hhHeader for MPIWorkPoolJobDistributor - intended for continuous resamplig jobs that spawn new jobs based on a pool/archive of structures
src/protocols/jd2/MultiThreadingJob.cc
src/protocols/jd2/MultiThreadingJob.fwd.hhHeader file for Job classes, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/MultiThreadingJob.hh
src/protocols/jd2/NoOutputJobOutputter.hhHeader file for NoOutputJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/NoOutputJobOutputterCreator.ccNoOutputJobOutputCreator class, part of November 2011 XRW2
src/protocols/jd2/NoOutputJobOutputterCreator.hh
src/protocols/jd2/Parser.ccAugust 2008 job distributor as planned at RosettaCon08 - Interface base class Parser
src/protocols/jd2/Parser.fwd.hhHeader file for Parser class, part of August 2008 job distributor
src/protocols/jd2/Parser.hhHeader file for Parser class, part of August 2008 job distributor
src/protocols/jd2/PDBJobInputter.ccAugust 2008 job distributor as planned at RosettaCon08 - Base class PDBJobInputter
src/protocols/jd2/PDBJobInputter.fwd.hhHeader file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/PDBJobInputter.hhHeader file for PDBJobInputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/PDBJobInputterCreator.hh
src/protocols/jd2/PDBJobOutputter.ccAugust 2008 job distributor as planned at RosettaCon08 - PDBJobOutputter
src/protocols/jd2/PDBJobOutputter.fwd.hhHeader file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/PDBJobOutputter.hhHeader file for PDBJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/PDBJobOutputterCreator.hh
src/protocols/jd2/PoseInputStreamJobInputter.cc
src/protocols/jd2/PoseInputStreamJobInputter.fwd.hh
src/protocols/jd2/PoseInputStreamJobInputter.hhHeader file for PoseInputStreamJobInputter class
src/protocols/jd2/PoseInputStreamJobInputterCreator.hh
src/protocols/jd2/ScoreMap.ccA place to put some common functions for scoremap output
src/protocols/jd2/ScoreMap.hhA place to put some common functions for scoremap output
src/protocols/jd2/ScoreOnlyJobOutputter.cc
src/protocols/jd2/ScoreOnlyJobOutputter.fwd.hh
src/protocols/jd2/ScoreOnlyJobOutputter.hh
src/protocols/jd2/ScoreOnlyJobOutputterCreator.hh
src/protocols/jd2/ShuffleJobDistributor.cc
src/protocols/jd2/ShuffleJobDistributor.hhImplementation of ShuffleFileSystemJobDistributor
src/protocols/jd2/SilentFileJobInputter.cc
src/protocols/jd2/SilentFileJobInputter.fwd.hh
src/protocols/jd2/SilentFileJobInputter.hhHeader file for SilentFileJobInputter class
src/protocols/jd2/SilentFileJobInputterCreator.hh
src/protocols/jd2/SilentFileJobOutputter.cc
src/protocols/jd2/SilentFileJobOutputter.fwd.hhHeader file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/SilentFileJobOutputter.hhHeader file for SilentFileJobOutputter class, part of August 2008 job distributor as planned at RosettaCon08
src/protocols/jd2/SilentFileJobOutputterCreator.hh
src/protocols/jd2/SingleFileBuffer.cc
src/protocols/jd2/SingleFileBuffer.fwd.hh
src/protocols/jd2/SingleFileBuffer.hh
src/protocols/jd2/util.cc
src/protocols/jd2/util.hh
src/protocols/jd2/archive/ArchiveBase.cc
src/protocols/jd2/archive/ArchiveBase.fwd.hh
src/protocols/jd2/archive/ArchiveBase.hh
src/protocols/jd2/archive/ArchiveManager.cc
src/protocols/jd2/archive/ArchiveManager.fwd.hh
src/protocols/jd2/archive/ArchiveManager.hh
src/protocols/jd2/archive/ArchiveMasterBase.cc
src/protocols/jd2/archive/ArchiveMasterBase.hh
src/protocols/jd2/archive/EvaluatedArchive.cc
src/protocols/jd2/archive/EvaluatedArchive.hh
src/protocols/jd2/archive/MPIArchiveJobDistributor.cc
src/protocols/jd2/archive/MPIArchiveJobDistributor.fwd.hh
src/protocols/jd2/archive/MPIArchiveJobDistributor.hh
src/protocols/jd2/parser/BluePrint.cc
src/protocols/jd2/parser/BluePrint.fwd.hh
src/protocols/jd2/parser/BluePrint.hh
src/protocols/jd2/parser/DataLoader.ccImplementation of the XML parser's DataLoader base class (ctor & dstor)
src/protocols/jd2/parser/DataLoader.fwd.hhForward declartion of the XML parser's DataLoader class
src/protocols/jd2/parser/DataLoader.hhDeclartion of the XML parser's DataLoader class
src/protocols/jd2/parser/DataLoaderCreator.ccCreator class for the parser's DataLoader classes
src/protocols/jd2/parser/DataLoaderCreator.hhCreator class for the parser's DataLoader classes
src/protocols/jd2/parser/DataLoaderFactory.ccImplementation of the factory class for the parser's DataLoader classes
src/protocols/jd2/parser/DataLoaderFactory.hhFactory class for the parser's DataLoader classes
src/protocols/jd2/parser/FragmentReader.cc
src/protocols/jd2/parser/FragmentReader.fwd.hh
src/protocols/jd2/parser/FragmentReader.hh
src/protocols/jd2/parser/FragSetLoader.cc
src/protocols/jd2/parser/FragSetLoader.hhDeclartion of the XML parser's FragSetLoader class for adding named FragSets to the DataMap
src/protocols/jd2/parser/MonteCarloLoader.cc
src/protocols/jd2/parser/MonteCarloLoader.hhDeclartion of the XML parser's MonteCarloLoader class for adding named ScoreFunctions to the DataMap
src/protocols/jd2/parser/ScoreFunctionLoader.cc
src/protocols/jd2/parser/ScoreFunctionLoader.hhDeclartion of the XML parser's ScoreFunctionLoader class for adding named ScoreFunctions to the DataMap
src/protocols/jd2/parser/StandardLoaderCreators.hh
src/protocols/jd2/parser/TaskOperationLoader.cc
src/protocols/jd2/parser/TaskOperationLoader.hhDeclartion of the XML parser's TaskOperationLoader class
src/protocols/jobdist/JobDistributors.cc
src/protocols/jobdist/JobDistributors.fwd.hh
src/protocols/jobdist/JobDistributors.hh
src/protocols/jobdist/Jobs.cc
src/protocols/jobdist/Jobs.fwd.hhObjects representing inputs for the JobDistributor
src/protocols/jobdist/Jobs.hhObjects representing inputs for the JobDistributor
src/protocols/jobdist/not_universal_main.ccSimple main method for applying a Mover to a set of input Poses
src/protocols/jobdist/not_universal_main.hhSimple main method for applying a Mover to a set of input Poses
src/protocols/jobdist/standard_mains.cc
src/protocols/jobdist/standard_mains.hhMain methods that implement the typical running patterns for executables
src/protocols/jumping/DisulfPairingLibrary.cc
src/protocols/jumping/DisulfPairingLibrary.hh
src/protocols/jumping/DisulfPairingsList.cc
src/protocols/jumping/DisulfPairingsList.fwd.hhFwd headers for ns jumping
src/protocols/jumping/DisulfPairingsList.hh
src/protocols/jumping/JumpSample.cc
src/protocols/jumping/JumpSample.hh
src/protocols/jumping/JumpSetup.cc
src/protocols/jumping/JumpSetup.fwd.hh
src/protocols/jumping/JumpSetup.hh
src/protocols/jumping/MembraneJump.cc
src/protocols/jumping/MembraneJump.fwd.hh
src/protocols/jumping/MembraneJump.hh
src/protocols/jumping/PairingLibrary.cc
src/protocols/jumping/PairingLibrary.fwd.hhFwd headers for ns jumping
src/protocols/jumping/PairingLibrary.hh
src/protocols/jumping/RandomSheetBuilder.ccSecondary structure will hold statistics about secondary structure predictions sources can be from
src/protocols/jumping/RandomSheetBuilder.hh
src/protocols/jumping/ResiduePairJump.ccClass to create jump transform from a pair of residues
src/protocols/jumping/ResiduePairJump.fwd.hh
src/protocols/jumping/ResiduePairJump.hhClass to create jump transform from a pair of residues
src/protocols/jumping/ResiduePairJumpSetup.cc
src/protocols/jumping/ResiduePairJumpSetup.fwd.hh
src/protocols/jumping/ResiduePairJumpSetup.hh
src/protocols/jumping/SameStrand.ccSecondary structure will hold statistics about secondary structure predictions sources can be from
src/protocols/jumping/SameStrand.fwd.hhFwd headers for ns jumping
src/protocols/jumping/SameStrand.hhSecondary structure will hold statistics about secondary structure predictions sources can be from
src/protocols/jumping/SheetBuilder.ccSecondary structure will hold statistics about secondary structure predictions sources can be from
src/protocols/jumping/SheetBuilder.hh
src/protocols/jumping/util.cc
src/protocols/jumping/util.hh
src/protocols/kinmatch/FunGroupTK.cc
src/protocols/kinmatch/FunGroupTK.hhToolKit for rapid IK based functional group placement
src/protocols/ligand_docking/AddHydrogen.ccLemmon
src/protocols/ligand_docking/AddHydrogen.fwd.hh
src/protocols/ligand_docking/AddHydrogen.hh
src/protocols/ligand_docking/AddHydrogens.ccLemmon
src/protocols/ligand_docking/AddHydrogens.fwd.hh
src/protocols/ligand_docking/AddHydrogens.hh
src/protocols/ligand_docking/AddHydrogensCreator.hhThis class will create instances of Mover AddHydrogens for the MoverFactory
src/protocols/ligand_docking/AtomCountFilter.ccFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/AtomCountFilter.hhFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/AtomCountFilterCreator.hhFilterCreator for the AtomCountFilter
src/protocols/ligand_docking/CompleteConnectionsFilter.cc
src/protocols/ligand_docking/CompleteConnectionsFilter.hh
src/protocols/ligand_docking/CompleteConnectionsFilterCreator.hhFilterCreator for the CompleteConnectionsFilter
src/protocols/ligand_docking/CompoundTranslate.cc
src/protocols/ligand_docking/CompoundTranslate.hh
src/protocols/ligand_docking/CompoundTranslateCreator.hhThis class will create instances of Mover CompoundTranslateCreator for the MoverFactory
src/protocols/ligand_docking/DistributionMap.cc
src/protocols/ligand_docking/DistributionMap.hh
src/protocols/ligand_docking/FinalMinimizer.cc
src/protocols/ligand_docking/FinalMinimizer.fwd.hh
src/protocols/ligand_docking/FinalMinimizer.hh
src/protocols/ligand_docking/FinalMinimizerCreator.hhThis class will create instances of Mover FinalMinimizerCreator for the MoverFactory
src/protocols/ligand_docking/grid_functions.cc
src/protocols/ligand_docking/grid_functions.hh
src/protocols/ligand_docking/GrowLigand.ccLemmon
src/protocols/ligand_docking/GrowLigand.fwd.hh
src/protocols/ligand_docking/GrowLigand.hh
src/protocols/ligand_docking/GrowLigandCreator.hhThis class will create instances of Mover GrowLigand for the MoverFactory
src/protocols/ligand_docking/HBondAcceptorFilter.ccFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/HBondAcceptorFilter.hhFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/HBondAcceptorFilterCreator.hhFilterCreator for the HBondAcceptorFilter
src/protocols/ligand_docking/HBondDonorFilter.ccFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/HBondDonorFilter.hhFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/HBondDonorFilterCreator.hhFilterCreator for the HBondDonorFilter
src/protocols/ligand_docking/HeavyAtomFilter.ccFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/HeavyAtomFilter.hhFind packing defects at an interface using packstat score terms
src/protocols/ligand_docking/HeavyAtomFilterCreator.hhFilterCreator for the HeavyAtomFilter
src/protocols/ligand_docking/HighResDocker.cc
src/protocols/ligand_docking/HighResDocker.fwd.hh
src/protocols/ligand_docking/HighResDocker.hh
src/protocols/ligand_docking/HighResDockerCreator.hhThis class will create instances of Mover HighResDockerCreator for the MoverFactory
src/protocols/ligand_docking/InterfaceBuilder.cc
src/protocols/ligand_docking/InterfaceBuilder.fwd.hh
src/protocols/ligand_docking/InterfaceBuilder.hh
src/protocols/ligand_docking/InterfaceScoreCalculator.cc
src/protocols/ligand_docking/InterfaceScoreCalculator.fwd.hh
src/protocols/ligand_docking/InterfaceScoreCalculator.hh
src/protocols/ligand_docking/InterfaceScoreCalculatorCreator.hhThis class will create instances of Mover InterfaceScoreCalculator for the MoverFactory
src/protocols/ligand_docking/ligand_dock_impl.cc
src/protocols/ligand_docking/ligand_dock_impl.hh
src/protocols/ligand_docking/ligand_functions.cc
src/protocols/ligand_docking/ligand_functions.hh
src/protocols/ligand_docking/ligand_scores.cc
src/protocols/ligand_docking/ligand_scores.hh
src/protocols/ligand_docking/LigandArea.cc
src/protocols/ligand_docking/LigandArea.fwd.hh
src/protocols/ligand_docking/LigandArea.hh
src/protocols/ligand_docking/LigandBaseProtocol.cc
src/protocols/ligand_docking/LigandBaseProtocol.hh
src/protocols/ligand_docking/LigandDesign.ccLemmon
src/protocols/ligand_docking/LigandDesign.fwd.hh
src/protocols/ligand_docking/LigandDesign.hh
src/protocols/ligand_docking/LigandDesignCreator.hhThis class will create instances of Mover LigandDesign for the MoverFactory
src/protocols/ligand_docking/LigandDockingLoaderCreators.hhCreator classes for the ligand docking DataLoader classes: InterfaceBuilderLoader and MoveMapBuilderLoader
src/protocols/ligand_docking/LigandDockingLoaders.ccImplementation of the InterfaceBuilderLoader and MoveMapBuilderLoader classes
src/protocols/ligand_docking/LigandDockingLoaders.hh
src/protocols/ligand_docking/LigandDockProtocol.cc
src/protocols/ligand_docking/LigandDockProtocol.fwd.hh
src/protocols/ligand_docking/LigandDockProtocol.hh
src/protocols/ligand_docking/MinimizeBackbone.cc
src/protocols/ligand_docking/MinimizeBackbone.fwd.hh
src/protocols/ligand_docking/MinimizeBackbone.hh
src/protocols/ligand_docking/MinimizeBackboneCreator.hhThis class will create instances of Mover MinimizeBackboneCreator for the MoverFactory
src/protocols/ligand_docking/MinimizeLigand.cc
src/protocols/ligand_docking/MinimizeLigand.fwd.hh
src/protocols/ligand_docking/MinimizeLigand.hh
src/protocols/ligand_docking/MoveMapBuilder.cc
src/protocols/ligand_docking/MoveMapBuilder.fwd.hh
src/protocols/ligand_docking/MoveMapBuilder.hh
src/protocols/ligand_docking/RandomConformerMover.cc
src/protocols/ligand_docking/RandomConformerMover.fwd.hh
src/protocols/ligand_docking/RandomConformerMover.hh
src/protocols/ligand_docking/RandomConformers.cc
src/protocols/ligand_docking/RandomConformers.hh
src/protocols/ligand_docking/RandomConformersCreator.hhThis class will create instances of Mover RandomConformersCreator for the MoverFactory
src/protocols/ligand_docking/ResidueTorsionRestraints.cc
src/protocols/ligand_docking/ResidueTorsionRestraints.fwd.hh
src/protocols/ligand_docking/ResidueTorsionRestraints.hh
src/protocols/ligand_docking/RigidSearchMover.cc
src/protocols/ligand_docking/RigidSearchMover.fwd.hh
src/protocols/ligand_docking/RigidSearchMover.hh
src/protocols/ligand_docking/Rotate.cc
src/protocols/ligand_docking/Rotate.fwd.hh
src/protocols/ligand_docking/Rotate.hh
src/protocols/ligand_docking/RotateCreator.hhThis class will create instances of Mover Rotate for the MoverFactory
src/protocols/ligand_docking/Rotates.cc
src/protocols/ligand_docking/Rotates.fwd.hh
src/protocols/ligand_docking/Rotates.hh
src/protocols/ligand_docking/RotatesCreator.hhThis class will create instances of Mover Rotates for the MoverFactory
src/protocols/ligand_docking/SlideTogether.cc
src/protocols/ligand_docking/SlideTogether.hh
src/protocols/ligand_docking/SlideTogetherCreator.hhThis class will create instances of Mover SlideTogether for the MoverFactory
src/protocols/ligand_docking/StartFrom.cc
src/protocols/ligand_docking/StartFrom.fwd.hh
src/protocols/ligand_docking/StartFrom.hhHeader of classes for resfile options
src/protocols/ligand_docking/StartFromCreator.hhThis class will create instances of Mover StartFrom for the MoverFactory
src/protocols/ligand_docking/TetherLigand.cc
src/protocols/ligand_docking/TetherLigand.fwd.hh
src/protocols/ligand_docking/TetherLigand.hh
src/protocols/ligand_docking/Transform.cc
src/protocols/ligand_docking/Transform.fwd.hh
src/protocols/ligand_docking/Transform.hh
src/protocols/ligand_docking/TransformCreator.hhThis class will create instances of Mover Transform for the MoverFactory
src/protocols/ligand_docking/Translate.cc
src/protocols/ligand_docking/Translate.fwd.hh
src/protocols/ligand_docking/Translate.hh
src/protocols/ligand_docking/TranslateCreator.hhThis class will create instances of Mover Translate for the MoverFactory
src/protocols/ligand_docking/UnconstrainedTorsionsMover.cc
src/protocols/ligand_docking/UnconstrainedTorsionsMover.fwd.hh
src/protocols/ligand_docking/UnconstrainedTorsionsMover.hh
src/protocols/ligand_docking/ligand_options/Interface.cc
src/protocols/ligand_docking/ligand_options/Interface.fwd.hh
src/protocols/ligand_docking/ligand_options/Interface.hh
src/protocols/ligand_docking/ligand_options/interface_distance_functions.cc
src/protocols/ligand_docking/ligand_options/interface_distance_functions.hh
src/protocols/loop_build/LoopBuild.cc
src/protocols/loop_build/LoopBuild.hh
src/protocols/loop_build/LoopMover_SlidingWindow.ccKinematic loop closure main protocols
src/protocols/loop_build/LoopMover_SlidingWindow.hh
src/protocols/loop_build/LoopMover_SlidingWindowCreator.cc
src/protocols/loop_build/LoopMover_SlidingWindowCreator.hhHeader for LoopMover_SlidingWindowCreator
src/protocols/loophash/BackboneDB.cc
src/protocols/loophash/BackboneDB.hhI little in the spirit of fragments but way more memory and speed efficient. Backbones are stored as 16bit fixed comma integers. :)
src/protocols/loophash/Exceptions.hh
src/protocols/loophash/FastGapMover.cc
src/protocols/loophash/FastGapMover.fwd.hhCloses gaps
src/protocols/loophash/FastGapMover.hhProtocols for closing gaps
src/protocols/loophash/LocalInserter.cc
src/protocols/loophash/LocalInserter.fwd.hhLocalInserter class forward declarations header
src/protocols/loophash/LocalInserter.hh
src/protocols/loophash/LoopHashInserter.fwd.hhLoopHashInserter class forward declarations header
src/protocols/loophash/LoopHashLibrary.cc
src/protocols/loophash/LoopHashLibrary.fwd.hhLoopHashLibrary class forward declarations header
src/protocols/loophash/LoopHashLibrary.hh
src/protocols/loophash/LoopHashMap.cc
src/protocols/loophash/LoopHashMap.hh
src/protocols/loophash/LoopHashMoverWrapper.cc
src/protocols/loophash/LoopHashMoverWrapper.hh
src/protocols/loophash/LoopHashMoverWrapperCreator.hh
src/protocols/loophash/LoopHashSampler.cc
src/protocols/loophash/LoopHashSampler.fwd.hhLoopHashSampler class forward declarations header
src/protocols/loophash/LoopHashSampler.hh
src/protocols/loophash/Mover_LoopHashRefine.cc
src/protocols/loophash/Mover_LoopHashRefine.hh
src/protocols/loophash/MPI_LoopHashRefine.cc
src/protocols/loophash/MPI_LoopHashRefine.hh
src/protocols/loophash/MPI_LoopHashRefine_Emperor.cc
src/protocols/loophash/MPI_LoopHashRefine_Emperor.hh
src/protocols/loophash/MPI_LoopHashRefine_Master.cc
src/protocols/loophash/MPI_LoopHashRefine_Master.hh
src/protocols/loophash/WorkUnit_LoopHash.cc
src/protocols/loophash/WorkUnit_LoopHash.hh
src/protocols/loops/Exceptions.hh
src/protocols/loops/FoldTreeFromLoopsWrapper.cc
src/protocols/loops/FoldTreeFromLoopsWrapper.fwd.hh
src/protocols/loops/FoldTreeFromLoopsWrapper.hh
src/protocols/loops/FoldTreeFromLoopsWrapperCreator.hh
src/protocols/loops/Loop.cc
src/protocols/loops/Loop.fwd.hhLoop class forward declarations header
src/protocols/loops/Loop.hh
src/protocols/loops/loopfinder.cc
src/protocols/loops/loopfinder.hh
src/protocols/loops/LoopMoverFactory.cc
src/protocols/loops/LoopMoverFactory.fwd.hhReport data to database
src/protocols/loops/LoopMoverFactory.hhFactory for creating LoopMover objects
src/protocols/loops/looprelax_protocols.cc
src/protocols/loops/looprelax_protocols.hh
src/protocols/loops/Loops.cc
src/protocols/loops/Loops.fwd.hhLoops and Loop class forward declarations header
src/protocols/loops/Loops.hh
src/protocols/loops/Loops.tmpl.hh
src/protocols/loops/loops_main.ccLoop building tools
src/protocols/loops/loops_main.hh
src/protocols/loops/LoopsFileIO.cc
src/protocols/loops/LoopsFileIO.fwd.hhLoopsFileIO forward declarations header
src/protocols/loops/LoopsFileIO.hhThis class exists to handle the reading and writing of loops files
src/protocols/loops/make_loops.cc
src/protocols/loops/make_loops.hh
src/protocols/loops/util.cc
src/protocols/loops/util.hh
src/protocols/loops/loop_closure/ccd/ccd_closure.cc
src/protocols/loops/loop_closure/ccd/ccd_closure.hh
src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.cc
src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.fwd.hhFwd headers for ns loops
src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.hhHeader file for CcdLoopClosureMover protocol
src/protocols/loops/loop_closure/ccd/FASelectSlidingWindowLoopClosure.cc
src/protocols/loops/loop_closure/ccd/FASelectSlidingWindowLoopClosure.fwd.hhFwd headers for FASelectSlidingWindowLoopClosure
src/protocols/loops/loop_closure/ccd/FASelectSlidingWindowLoopClosure.hh
src/protocols/loops/loop_closure/ccd/LoopClosure.cc
src/protocols/loops/loop_closure/ccd/LoopClosure.fwd.hhFwd headers for ns loops
src/protocols/loops/loop_closure/ccd/LoopClosure.hh
src/protocols/loops/loop_closure/ccd/ShortLoopClosure.cc
src/protocols/loops/loop_closure/ccd/ShortLoopClosure.fwd.hh
src/protocols/loops/loop_closure/ccd/ShortLoopClosure.hh
src/protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.cc
src/protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.fwd.hhFwd headers for ns loops
src/protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.hhHeader file for SlidingWindowLoopClosure protocol
src/protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.cc
src/protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.fwd.hhFwd headers for ns loops
src/protocols/loops/loop_closure/ccd/WidthFirstSlidingWindowLoopClosure.hh
src/protocols/loops/loop_closure/kinematic_closure/KinematicMover.cc
src/protocols/loops/loop_closure/kinematic_closure/KinematicMover.fwd.hhKinematicMover forward declarations header
src/protocols/loops/loop_closure/kinematic_closure/KinematicMover.hh
src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.ccImplementations for KinematicPerturbers used by the kinematic mover
src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.fwd.hhKinematicPerturber forward declarations header
src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.hhHeader file for KinematicPerturbers used by the kineamtic mover
src/protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.ccKinematicWrapper methods implemented - this is a mover which simplifies use of KinematicMover loop modeling
src/protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.fwd.hhKinematicWrapper forward declarations header
src/protocols/loops/loop_closure/kinematic_closure/KinematicWrapper.hhWrapper for KinematicMover - useful when only apply() is available
src/protocols/loops/loop_mover/IndependentLoopMover.ccLoop mover base class
src/protocols/loops/loop_mover/IndependentLoopMover.fwd.hh
src/protocols/loops/loop_mover/IndependentLoopMover.hh
src/protocols/loops/loop_mover/LoopMover.ccLoop mover base class
src/protocols/loops/loop_mover/LoopMover.fwd.hhLoopMover base classes
src/protocols/loops/loop_mover/LoopMover.hh
src/protocols/loops/loop_mover/perturb/LoopMover_CCD.cc
src/protocols/loops/loop_mover/perturb/LoopMover_CCD.fwd.hhLoopMover_Perutrb_CCD forward declaration
src/protocols/loops/loop_mover/perturb/LoopMover_CCD.hh
src/protocols/loops/loop_mover/perturb/LoopMover_CCDCreator.hhHeader for LoopMover_CCDCreator
src/protocols/loops/loop_mover/perturb/LoopMover_KIC.cc
src/protocols/loops/loop_mover/perturb/LoopMover_KIC.fwd.hhLoopMover_Perturb_KIC forward declaration
src/protocols/loops/loop_mover/perturb/LoopMover_KIC.hh
src/protocols/loops/loop_mover/perturb/LoopMover_KICCreator.hh
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD.cc
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD.fwd.hhLoopMover_QuickCCD forward declaration
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD.hh
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD_Moves.cc
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD_Moves.fwd.hhLoopMover_QuickCCD_Moves forward declaration
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD_Moves.hh
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD_MovesCreator.hh
src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCDCreator.hhHeader for LoopMover_QuickCCDCreator
src/protocols/loops/loop_mover/refine/LoopMover_Backrub.cc
src/protocols/loops/loop_mover/refine/LoopMover_Backrub.fwd.hhLoopMover_Backrub forward declaration
src/protocols/loops/loop_mover/refine/LoopMover_Backrub.hh
src/protocols/loops/loop_mover/refine/LoopMover_BackrubCreator.hhHeader for LoopMover_BackrubCreator
src/protocols/loops/loop_mover/refine/LoopMover_CCD.cc
src/protocols/loops/loop_mover/refine/LoopMover_CCD.fwd.hh
src/protocols/loops/loop_mover/refine/LoopMover_CCD.hh
src/protocols/loops/loop_mover/refine/LoopMover_CCDCreator.hh
src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc
src/protocols/loops/loop_mover/refine/LoopMover_KIC.fwd.hhLoopMover_Backrub forward declaration
src/protocols/loops/loop_mover/refine/LoopMover_KIC.hh
src/protocols/loops/loop_mover/refine/LoopMover_KICCreator.hh
src/protocols/make_rot_lib/MakeRotLib.cc
src/protocols/make_rot_lib/MakeRotLib.hh
src/protocols/make_rot_lib/RotData.cc
src/protocols/make_rot_lib/RotData.hh
src/protocols/match/BumpGrid.cc
src/protocols/match/BumpGrid.fwd.hh
src/protocols/match/BumpGrid.hh
src/protocols/match/Hit.ccConstructors for match_dspos1
src/protocols/match/Hit.fwd.hhHit class forward declaration
src/protocols/match/Hit.hhHit typedef
src/protocols/match/Matcher.cc
src/protocols/match/Matcher.fwd.hh
src/protocols/match/Matcher.hh
src/protocols/match/MatcherMover.ccImplementation of mover wrapper for matcher
src/protocols/match/MatcherMover.fwd.hh
src/protocols/match/MatcherMover.hh
src/protocols/match/MatcherMoverCreator.hhThis class will create instances of Mover FlxbbDesign for the MoverFactory
src/protocols/match/MatcherTask.cc
src/protocols/match/MatcherTask.fwd.hh
src/protocols/match/MatcherTask.hh
src/protocols/match/MatchPositionModifiers.ccImplementations for MatchPositionModifiers
src/protocols/match/MatchPositionModifiers.fwd.hhForward declaration for MatchPositionModifiers
src/protocols/match/MatchPositionModifiers.hhHeader file for MatchPositionModifiers
src/protocols/match/MatchSet.cc
src/protocols/match/MatchSet.fwd.hh
src/protocols/match/MatchSet.hh
src/protocols/match/OccupiedSpaceHash.ccDeclaration for classes in 6D hasher
src/protocols/match/OccupiedSpaceHash.fwd.hh
src/protocols/match/OccupiedSpaceHash.hhDeclaration for classes in 6D hasher
src/protocols/match/VoxelSetIterator.ccImplementation of the VoxelSetIterator class
src/protocols/match/VoxelSetIterator.fwd.hh
src/protocols/match/VoxelSetIterator.hhForward declaration for iterator to traverse the 64 bins each hit covers
src/protocols/match/downstream/ActiveSiteGrid.cc
src/protocols/match/downstream/ActiveSiteGrid.fwd.hh
src/protocols/match/downstream/ActiveSiteGrid.hh
src/protocols/match/downstream/ClassicMatchAlgorithm.cc
src/protocols/match/downstream/ClassicMatchAlgorithm.fwd.hh
src/protocols/match/downstream/ClassicMatchAlgorithm.hh
src/protocols/match/downstream/DownstreamAlgorithm.cc
src/protocols/match/downstream/DownstreamAlgorithm.fwd.hh
src/protocols/match/downstream/DownstreamAlgorithm.hhDeclaration for the base-class algorithm that creates hits from an upstream builder, while managing the logic of their creation. Furthermore, the downstream algorithm manages update of hits from previous rounds should they loose their potential to result in matches
src/protocols/match/downstream/DownstreamBuilder.cc
src/protocols/match/downstream/DownstreamBuilder.fwd.hh
src/protocols/match/downstream/DownstreamBuilder.hh
src/protocols/match/downstream/GeometrySecMatchRPE.cc
src/protocols/match/downstream/GeometrySecMatchRPE.fwd.hh
src/protocols/match/downstream/GeometrySecMatchRPE.hh
src/protocols/match/downstream/LigandConformerBuilder.cc
src/protocols/match/downstream/LigandConformerBuilder.fwd.hh
src/protocols/match/downstream/LigandConformerBuilder.hh
src/protocols/match/downstream/RigidLigandBuilder.cc
src/protocols/match/downstream/RigidLigandBuilder.fwd.hh
src/protocols/match/downstream/RigidLigandBuilder.hh
src/protocols/match/downstream/ScoringSecMatchRPE.cc
src/protocols/match/downstream/ScoringSecMatchRPE.fwd.hh
src/protocols/match/downstream/ScoringSecMatchRPE.hh
src/protocols/match/downstream/SecMatchEvaluatorFactory.cc
src/protocols/match/downstream/SecMatchEvaluatorFactory.hh
src/protocols/match/downstream/SecMatchResiduePairEvaluator.cc
src/protocols/match/downstream/SecMatchResiduePairEvaluator.fwd.hh
src/protocols/match/downstream/SecMatchResiduePairEvaluator.hh
src/protocols/match/downstream/SecondaryMatcherToDownstreamResidue.ccClass implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round
src/protocols/match/downstream/SecondaryMatcherToDownstreamResidue.fwd.hh
src/protocols/match/downstream/SecondaryMatcherToDownstreamResidue.hhClass declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round
src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.ccClass implementation for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round
src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.fwd.hh
src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.hhClass declaration for secondary matcher that generates upstream-only hits matching the geometry of one upstream residue with another upstream residue generated in a previous round
src/protocols/match/output/DownstreamRMSEvaluator.cc
src/protocols/match/output/DownstreamRMSEvaluator.fwd.hh
src/protocols/match/output/DownstreamRMSEvaluator.hh
src/protocols/match/output/LimitHitsPerRotamerFilter.cc
src/protocols/match/output/LimitHitsPerRotamerFilter.fwd.hh
src/protocols/match/output/LimitHitsPerRotamerFilter.hh
src/protocols/match/output/MatchConsolidator.cc
src/protocols/match/output/MatchConsolidator.fwd.hh
src/protocols/match/output/MatchConsolidator.hh
src/protocols/match/output/MatchEvaluator.cc
src/protocols/match/output/MatchEvaluator.fwd.hhForward declaration for abstract class to filter matches
src/protocols/match/output/MatchEvaluator.hh
src/protocols/match/output/MatchFilter.ccImplementation for abstract filter class
src/protocols/match/output/MatchFilter.fwd.hhForward declaration for abstract class to filter matches
src/protocols/match/output/MatchFilter.hhDeclaration for abstract class to filter matches
src/protocols/match/output/MatchGrouper.cc
src/protocols/match/output/MatchGrouper.fwd.hh
src/protocols/match/output/MatchGrouper.hh
src/protocols/match/output/MatchOutputter.ccImplementation of class to write output matches that pass filters This class does not "look ahead" to future matches to decide whether the current match to process should be output, however, filters are able to keep a history of what they've output so far
src/protocols/match/output/MatchOutputter.fwd.hhForward declaration for no-lookahead match processor
src/protocols/match/output/MatchOutputter.hh
src/protocols/match/output/MatchProcessor.cc
src/protocols/match/output/MatchProcessor.fwd.hh
src/protocols/match/output/MatchProcessor.hh
src/protocols/match/output/OutputWriter.ccImplementation for the class to write output matches that have (presumably) passed the output filters
src/protocols/match/output/OutputWriter.fwd.hhForward declaration of class to write output matches that have (presumably) passed the output filters
src/protocols/match/output/OutputWriter.hh
src/protocols/match/output/PDBWriter.ccForward declaration of class to write output matches that have (presumably) passed the output filters
src/protocols/match/output/PDBWriter.fwd.hh
src/protocols/match/output/PDBWriter.hh
src/protocols/match/output/PoseInserter.cc
src/protocols/match/output/PoseInserter.fwd.hh
src/protocols/match/output/PoseInserter.hh
src/protocols/match/output/ProcessorFactory.cc
src/protocols/match/output/ProcessorFactory.fwd.hh
src/protocols/match/output/ProcessorFactory.hhImplementation for a factory class responsible for instantiating MatchProcessor classes
src/protocols/match/output/SameChiBinComboGrouper.cc
src/protocols/match/output/SameChiBinComboGrouper.fwd.hh
src/protocols/match/output/SameChiBinComboGrouper.hh
src/protocols/match/output/SameRotamerComboGrouper.cc
src/protocols/match/output/SameRotamerComboGrouper.fwd.hh
src/protocols/match/output/SameRotamerComboGrouper.hh
src/protocols/match/output/SameSequenceGrouper.cc
src/protocols/match/output/SameSequenceGrouper.fwd.hh
src/protocols/match/output/SameSequenceGrouper.hh
src/protocols/match/output/UpstreamCollisionFilter.cc
src/protocols/match/output/UpstreamCollisionFilter.fwd.hhForward declaration for abstract class to filter matches
src/protocols/match/output/UpstreamCollisionFilter.hhImplementation for class to filter matches where the upstream residues collide
src/protocols/match/output/UpstreamDownstreamCollisionFilter.cc
src/protocols/match/output/UpstreamDownstreamCollisionFilter.fwd.hhForward declaration for abstract class to filter matches
src/protocols/match/output/UpstreamDownstreamCollisionFilter.hhImplementation for class to filter matches where the upstream residues collide
src/protocols/match/output/UpstreamHitCacher.cc
src/protocols/match/output/UpstreamHitCacher.fwd.hhForward declaration for class to cache and recall the conformations of upstream hits
src/protocols/match/output/UpstreamHitCacher.hhDeclaration for class to cache and recall the conformations of upstream hits
src/protocols/match/output/WriteKinemageOutputter.ccForward declaration of class to write output matches that have (presumably) passed the output filters
src/protocols/match/output/WriteKinemageOutputter.fwd.hh
src/protocols/match/output/WriteKinemageOutputter.hh
src/protocols/match/output/WriteUpstreamCoordinateKineamge.cc
src/protocols/match/output/WriteUpstreamCoordinateKineamge.fwd.hh
src/protocols/match/output/WriteUpstreamCoordinateKineamge.hh
src/protocols/match/upstream/OriginalScaffoldBuildPoint.cc
src/protocols/match/upstream/OriginalScaffoldBuildPoint.fwd.hh
src/protocols/match/upstream/OriginalScaffoldBuildPoint.hh
src/protocols/match/upstream/ProteinSCSampler.ccClass declarations for base class and simple derived class for SC sampling
src/protocols/match/upstream/ProteinSCSampler.fwd.hhForward declaration for base class and simple derived class for SC sampling in matcher
src/protocols/match/upstream/ProteinSCSampler.hhClass declarations for base class and simple derived class for SC sampling
src/protocols/match/upstream/ProteinUpstreamBuilder.cc
src/protocols/match/upstream/ProteinUpstreamBuilder.fwd.hh
src/protocols/match/upstream/ProteinUpstreamBuilder.hh
src/protocols/match/upstream/ScaffoldBuildPoint.cc
src/protocols/match/upstream/ScaffoldBuildPoint.fwd.hh
src/protocols/match/upstream/ScaffoldBuildPoint.hh
src/protocols/match/upstream/UpstreamBuilder.cc
src/protocols/match/upstream/UpstreamBuilder.fwd.hh
src/protocols/match/upstream/UpstreamBuilder.hh
src/protocols/match/upstream/UpstreamResTypeGeometry.cc
src/protocols/match/upstream/UpstreamResTypeGeometry.fwd.hhForward declaration for class to measure the geometry of a given ResidueType
src/protocols/match/upstream/UpstreamResTypeGeometry.hh
src/protocols/medal/MedalExchangeMover.cc
src/protocols/medal/MedalExchangeMover.fwd.hh
src/protocols/medal/MedalExchangeMover.hh
src/protocols/medal/MedalMain.cc
src/protocols/medal/MedalMain.hh
src/protocols/medal/MedalMover.cc
src/protocols/medal/MedalMover.fwd.hh
src/protocols/medal/MedalMover.hh
src/protocols/medal/util.cc
src/protocols/medal/util.hh
src/protocols/motifs/BuildPosition.ccPosition where motifs are built in MotifSearch
src/protocols/motifs/BuildPosition.fwd.hhForward declaration for position where motifs are built in MotifSearch
src/protocols/motifs/BuildPosition.hhClass declaration for position where motifs are built in MotifSearch
src/protocols/motifs/IRCollection.ccImplmentation of interaction motifs
src/protocols/motifs/IRCollection.fwd.hhForward declaration for sets of interaction motifis between residues
src/protocols/motifs/IRCollection.hhClass declaration for collections of inverse rotamers
src/protocols/motifs/LigandMotifSearch.ccLigand motif searching protocol
src/protocols/motifs/LigandMotifSearch.fwd.hhForward declaration for interaction motif search protocol
src/protocols/motifs/LigandMotifSearch.hhClass declaration for ligand motif searching protocol
src/protocols/motifs/Motif.ccImplementation of interaction motifs
src/protocols/motifs/Motif.fwd.hhForward declaration for interaction motif between residues
src/protocols/motifs/Motif.hhHeader for interaction motif between residues
src/protocols/motifs/motif_utils.ccMotif helper/conversion/io functions
src/protocols/motifs/motif_utils.hhHeader for motif helper/conversion/io functions
src/protocols/motifs/MotifDnaPacker.cc
src/protocols/motifs/MotifDnaPacker.fwd.hh
src/protocols/motifs/MotifDnaPacker.hh
src/protocols/motifs/MotifDnaPackerCreator.hhThis class will create instances of Mover MotifDnaPacker for the MoverFactory
src/protocols/motifs/MotifHit.ccClass that holds information about a motif in the context of the search
src/protocols/motifs/MotifHit.fwd.hhForward declaration for class that holds information about a motif in the context of the search
src/protocols/motifs/MotifHit.hhClass declaration for class that holds information about a motif in the context of the search
src/protocols/motifs/MotifLibrary.ccImplementation of interaction motifs
src/protocols/motifs/MotifLibrary.fwd.hhForward declaration for sets of interaction motifis between residues
src/protocols/motifs/MotifLibrary.hhClass declaration for sets of interaction motifs between residues
src/protocols/motifs/MotifSearch.ccMotif searching protocol
src/protocols/motifs/MotifSearch.fwd.hhForward declaration for interaction motif search protocol
src/protocols/motifs/MotifSearch.hhClass declaration for motif searching protocol
src/protocols/motifs/SingleMotif.cc
src/protocols/motifs/SingleMotif.fwd.hhForward declaration for interaction motif between residues
src/protocols/motifs/SingleMotif.hhHeader for interaction motif between residues
src/protocols/motifs/useful_code.cc
src/protocols/moves/BoolMover.cc
src/protocols/moves/BoolMover.hh
src/protocols/moves/CanonicalSamplingMover.cc
src/protocols/moves/CanonicalSamplingMover.fwd.hh
src/protocols/moves/CanonicalSamplingMover.hh
src/protocols/moves/ChangeFoldTreeMover.fwd.hh
src/protocols/moves/ChangeFoldTreeMover.hhChangeFoldTreeMover
src/protocols/moves/CompositionMover.cc
src/protocols/moves/CompositionMover.fwd.hh
src/protocols/moves/CompositionMover.hh
src/protocols/moves/CyclicMover.cc
src/protocols/moves/CyclicMover.fwd.hh
src/protocols/moves/CyclicMover.hh
src/protocols/moves/DataMap.cc
src/protocols/moves/DataMap.fwd.hh
src/protocols/moves/DataMap.hh
src/protocols/moves/DataMapObj.hh
src/protocols/moves/DsspMover.ccPerforms dssp and set secondary structure to pose
src/protocols/moves/DsspMover.fwd.hh
src/protocols/moves/DsspMover.hhHeader file of DsspMover.cc
src/protocols/moves/DsspMoverCreator.hh
src/protocols/moves/FilterMover.cc
src/protocols/moves/FilterMover.fwd.hh
src/protocols/moves/FilterMover.hh
src/protocols/moves/GenericMonteCarloMover.ccPerform a given mover and sample structures by MonteCarlo
src/protocols/moves/GenericMonteCarloMover.fwd.hh
src/protocols/moves/GenericMonteCarloMover.hhPerform a given mover and sample structures by MonteCarlo
src/protocols/moves/GenericMonteCarloMoverCreator.hh
src/protocols/moves/IfMover.cc
src/protocols/moves/IfMover.hh
src/protocols/moves/IfMoverCreator.hh
src/protocols/moves/IteratedConvergenceMover.ccImplementation of IteratedConvergenceMover, class to repeatedly apply a submover until filter convergence is reached
src/protocols/moves/IteratedConvergenceMover.fwd.hhForward declaration of the mover class to repeatedly apply a submover until filter convergence is reached
src/protocols/moves/IteratedConvergenceMover.hhMover class to repeatedly apply a submover until filter convergence is reached
src/protocols/moves/IteratedConvergenceMoverCreator.hhThis class will create instances of Mover IteratedConvergenceMover for the MoverFactory
src/protocols/moves/JumpOutMover.cc
src/protocols/moves/JumpOutMover.fwd.hh
src/protocols/moves/JumpOutMover.hhJumpOutMover
src/protocols/moves/MonteCarlo.cc
src/protocols/moves/MonteCarlo.fwd.hh
src/protocols/moves/MonteCarlo.hh
src/protocols/moves/MonteCarlo.tmpl.hhImplentation for MonteCarlo template functions
src/protocols/moves/MonteCarloExceptionConverge.fwd.hh
src/protocols/moves/MonteCarloExceptionConverge.hh
src/protocols/moves/MonteCarloRecover.cc
src/protocols/moves/MonteCarloRecover.fwd.hh
src/protocols/moves/MonteCarloRecover.hh
src/protocols/moves/MonteCarloRecoverCreator.hh
src/protocols/moves/MonteCarloStatus.hh
src/protocols/moves/MonteCarloTest.cc
src/protocols/moves/MonteCarloTest.fwd.hh
src/protocols/moves/MonteCarloTest.hhPerform a given mover and sample structures by MonteCarlo
src/protocols/moves/MonteCarloTestCreator.hh
src/protocols/moves/Mover.ccMethod code and full headers for Mover-- keeps heavily-included Mover.hh small and concise to maximize compiling efficiency and to make the class definitions easier to read
src/protocols/moves/Mover.fwd.hh
src/protocols/moves/Mover.hh
src/protocols/moves/MoverContainer.ccApply functions for classes of type MoverContainer
src/protocols/moves/MoverContainer.fwd.hhMoverContainer forward declarations header
src/protocols/moves/MoverContainer.hhBase class for containers of movers such as SequenceMover
src/protocols/moves/MoverContainerCreator.hh
src/protocols/moves/MoverCreator.cc
src/protocols/moves/MoverCreator.hhBase class for MoverCreators for the Mover load-time factory registration scheme
src/protocols/moves/MoverFactory.cc
src/protocols/moves/MoverFactory.fwd.hh
src/protocols/moves/MoverFactory.hh
src/protocols/moves/MoverStatistics.ccKeeps track of the acceptance_rate of a Mover
src/protocols/moves/MoverStatistics.hhKeeps track of the acceptance_rate of a Mover
src/protocols/moves/MoverStatus.cc
src/protocols/moves/MoverStatus.hhReturn status enum for Movers
src/protocols/moves/NullMover.cc
src/protocols/moves/NullMover.fwd.hh
src/protocols/moves/NullMover.hh
src/protocols/moves/OutputMovers.ccFile to contain classes that deal with output and pdb dumping
src/protocols/moves/OutputMovers.fwd.hhOutputMovers forward declarations header
src/protocols/moves/OutputMovers.hhFile to contain classes that deal with output and pdb dumping
src/protocols/moves/PyMolMover.ccSend infromation to PyMol
src/protocols/moves/PyMolMover.fwd.hh
src/protocols/moves/PyMolMover.hhSend infromation to PyMol
src/protocols/moves/RampingMover.ccMover class for ramping the repulsive term of a score function over the course of several apply() evaluations
src/protocols/moves/RampingMover.fwd.hh
src/protocols/moves/RampingMover.hh
src/protocols/moves/RepeatMover.cc
src/protocols/moves/RepeatMover.fwd.hh
src/protocols/moves/RepeatMover.hh
src/protocols/moves/ReplicaExchangeMC.ccImplementing a Recplica Exchange Monte Carlo Mover
src/protocols/moves/ReplicaExchangeMC.fwd.hhImplementing a Recplica Exchange Monte Carlo Mover
src/protocols/moves/ReplicaExchangeMC.hhImplementing a Recplica Exchange Monte Carlo Mover
src/protocols/moves/ResId.cc
src/protocols/moves/ResId.fwd.hh
src/protocols/moves/ResId.hhA simple base class providing common access to a residue identity for movers and filters. The anticipated usage is to derive movers and filters multiply, from the relevant base class and from ResId and make these movers/filters use the residue id encapsulated in this class
src/protocols/moves/StructureRestrictor.ccLookup relevant chains for a structure in a table
src/protocols/moves/StructureRestrictor.fwd.hhLookup relevant chains for a structure in a table
src/protocols/moves/StructureRestrictor.hhLookup relevant chains for a structure in a table
src/protocols/moves/TemperatuerController.fwd.hh
src/protocols/moves/TrialCounter.cc
src/protocols/moves/TrialCounter.hh
src/protocols/moves/TrialMover.cc
src/protocols/moves/TrialMover.fwd.hhTrialMover forward declarations header
src/protocols/moves/TrialMover.hh
src/protocols/moves/util.cc
src/protocols/moves/util.hh
src/protocols/moves/WhileMover.cc
src/protocols/moves/WhileMover.fwd.hh
src/protocols/moves/WhileMover.hh
src/protocols/moves/mc_convergence_checks/ConvergenceCheck.fwd.hh
src/protocols/moves/mc_convergence_checks/ConvergenceCheck.hh
src/protocols/multistate_design/MetricCalculatorFitnessFunction.cc
src/protocols/multistate_design/MetricCalculatorFitnessFunction.fwd.hh
src/protocols/multistate_design/MetricCalculatorFitnessFunction.hh
src/protocols/multistate_design/MultiStateAggregateFunction.cc
src/protocols/multistate_design/MultiStateAggregateFunction.fwd.hh
src/protocols/multistate_design/MultiStateAggregateFunction.hh
src/protocols/multistate_design/MultiStateEntity.cc
src/protocols/multistate_design/MultiStateEntity.fwd.hh
src/protocols/multistate_design/MultiStateEntity.hh
src/protocols/multistate_design/MultiStateFitnessFunction.cc
src/protocols/multistate_design/MultiStateFitnessFunction.fwd.hh
src/protocols/multistate_design/MultiStateFitnessFunction.hh
src/protocols/multistate_design/MultiStatePacker.cc
src/protocols/multistate_design/MultiStatePacker.fwd.hh
src/protocols/multistate_design/MultiStatePacker.hh
src/protocols/multistate_design/PackingState.cc
src/protocols/multistate_design/PackingState.fwd.hh
src/protocols/multistate_design/PackingState.hhFor multistate design that is based on (re)use of packer information (RotamerSets and InteractionGraph)
src/protocols/multistate_design/PartitionAggregateFunction.cc
src/protocols/multistate_design/PartitionAggregateFunction.fwd.hh
src/protocols/multistate_design/PartitionAggregateFunction.hh
src/protocols/multistate_design/SingleState.cc
src/protocols/multistate_design/SingleState.fwd.hh
src/protocols/multistate_design/SingleState.hh
src/protocols/multistate_design/SingleStateEntityData.cc
src/protocols/multistate_design/SingleStateEntityData.fwd.hh
src/protocols/multistate_design/SingleStateEntityData.hh
src/protocols/multistate_design/SingleStateFitnessFunction.cc
src/protocols/multistate_design/SingleStateFitnessFunction.fwd.hh
src/protocols/multistate_design/SingleStateFitnessFunction.hh
src/protocols/multistate_design/util.ccCollection of useful utilities for setting up and using a GeneticAlgorithm with multistate design
src/protocols/multistate_design/util.hh
src/protocols/noesy_assign/Assignment.cc
src/protocols/noesy_assign/Assignment.fwd.hh
src/protocols/noesy_assign/Assignment.hh
src/protocols/noesy_assign/CrossPeak.cc
src/protocols/noesy_assign/CrossPeak.fwd.hh
src/protocols/noesy_assign/CrossPeak.hh
src/protocols/noesy_assign/CrossPeakInfo.cc
src/protocols/noesy_assign/CrossPeakInfo.fwd.hh
src/protocols/noesy_assign/CrossPeakInfo.hh
src/protocols/noesy_assign/CrossPeakList.cc
src/protocols/noesy_assign/CrossPeakList.fwd.hh
src/protocols/noesy_assign/CrossPeakList.hh
src/protocols/noesy_assign/CrossPeakList.impl.hh
src/protocols/noesy_assign/CyanaModule.cc
src/protocols/noesy_assign/CyanaModule.hh
src/protocols/noesy_assign/DistanceScoreMover.cc
src/protocols/noesy_assign/DistanceScoreMover.fwd.hh
src/protocols/noesy_assign/DistanceScoreMover.hh
src/protocols/noesy_assign/Exceptions.hh
src/protocols/noesy_assign/NoesyModule.ccMain hook-up for the automatic NOESY assignment module
src/protocols/noesy_assign/NoesyModule.fwd.hh
src/protocols/noesy_assign/NoesyModule.hhMain hook-up for the automatic NOESY assignment module
src/protocols/noesy_assign/NoesyModule.impl.hh
src/protocols/noesy_assign/PeakAssignment.cc
src/protocols/noesy_assign/PeakAssignment.fwd.hh
src/protocols/noesy_assign/PeakAssignment.hh
src/protocols/noesy_assign/PeakAssignmentParameters.cc
src/protocols/noesy_assign/PeakAssignmentParameters.hh
src/protocols/noesy_assign/PeakAssignmentResidueMap.cc
src/protocols/noesy_assign/PeakAssignmentResidueMap.fwd.hh
src/protocols/noesy_assign/PeakAssignmentResidueMap.hh
src/protocols/noesy_assign/PeakCalibrator.cc
src/protocols/noesy_assign/PeakCalibrator.fwd.hh
src/protocols/noesy_assign/PeakCalibrator.hh
src/protocols/noesy_assign/PeakFileFormat.cc
src/protocols/noesy_assign/PeakFileFormat.fwd.hh
src/protocols/noesy_assign/PeakFileFormat.hh
src/protocols/noesy_assign/PeakFileFormat_Sparky.cc
src/protocols/noesy_assign/PeakFileFormat_Sparky.hh
src/protocols/noesy_assign/PeakFileFormat_xpk.cc
src/protocols/noesy_assign/PeakFileFormat_xpk.hh
src/protocols/noesy_assign/Resonance.cc
src/protocols/noesy_assign/Resonance.hh
src/protocols/noesy_assign/ResonanceList.cc
src/protocols/noesy_assign/ResonanceList.fwd.hh
src/protocols/noesy_assign/ResonanceList.hhTable with atomID - chemical shift mapping
src/protocols/noesy_assign/StructureDependentPeakCalibrator.cc
src/protocols/noesy_assign/StructureDependentPeakCalibrator.hh
src/protocols/noesy_assign/StructureIndependentPeakCalibrator.cc
src/protocols/noesy_assign/StructureIndependentPeakCalibrator.hh
src/protocols/noesy_assign/util.cc
src/protocols/noesy_assign/util.hh
src/protocols/nonlocal/BiasedFragmentMover.cc
src/protocols/nonlocal/BiasedFragmentMover.fwd.hh
src/protocols/nonlocal/BiasedFragmentMover.hh
src/protocols/nonlocal/Chunk.cc
src/protocols/nonlocal/Chunk.fwd.hh
src/protocols/nonlocal/Chunk.hh
src/protocols/nonlocal/HelixRotate.cc
src/protocols/nonlocal/HelixRotate.fwd.hh
src/protocols/nonlocal/HelixRotate.hh
src/protocols/nonlocal/Policy.fwd.hh
src/protocols/nonlocal/Policy.hh
src/protocols/nonlocal/PolicyFactory.cc
src/protocols/nonlocal/PolicyFactory.hh
src/protocols/nonlocal/Region.cc
src/protocols/nonlocal/Region.fwd.hh
src/protocols/nonlocal/Region.hh
src/protocols/nonlocal/SheetTranslate.cc
src/protocols/nonlocal/SheetTranslate.fwd.hh
src/protocols/nonlocal/SheetTranslate.hh
src/protocols/nonlocal/SimpleTreeBuilder.cc
src/protocols/nonlocal/SimpleTreeBuilder.fwd.hh
src/protocols/nonlocal/SimpleTreeBuilder.hh
src/protocols/nonlocal/SingleFragmentMover.cc
src/protocols/nonlocal/SingleFragmentMover.fwd.hh
src/protocols/nonlocal/SingleFragmentMover.hh
src/protocols/nonlocal/SingleFragmentMoverCreator.cc
src/protocols/nonlocal/SingleFragmentMoverCreator.hh
src/protocols/nonlocal/SmoothPolicy.cc
src/protocols/nonlocal/SmoothPolicy.hh
src/protocols/nonlocal/StarTreeBuilder.cc
src/protocols/nonlocal/StarTreeBuilder.fwd.hh
src/protocols/nonlocal/StarTreeBuilder.hh
src/protocols/nonlocal/TreeBuilder.fwd.hh
src/protocols/nonlocal/TreeBuilder.hh
src/protocols/nonlocal/TreeBuilderFactory.cc
src/protocols/nonlocal/TreeBuilderFactory.hh
src/protocols/nonlocal/UniformPolicy.cc
src/protocols/nonlocal/UniformPolicy.hh
src/protocols/nonlocal/util.cc
src/protocols/nonlocal/util.hh
src/protocols/optimize_weights/DDGBindOptEData.cc
src/protocols/optimize_weights/DDGBindOptEData.fwd.hhForward header for a optE position data class that holds interface ddG information
src/protocols/optimize_weights/DDGBindOptEData.hhHeader file for OptEPositionData class that hold interface ddG information
src/protocols/optimize_weights/DGBindOptEData.ccImplementation of the OptEPositionData class that handles interface ddG optimization
src/protocols/optimize_weights/DGBindOptEData.fwd.hh
src/protocols/optimize_weights/DGBindOptEData.hh
src/protocols/optimize_weights/IterativeOptEDriver.ccImplementation of iterative weight fitting protocol
src/protocols/optimize_weights/IterativeOptEDriver.fwd.hhForward declaration of iterative weight fitting protocol
src/protocols/optimize_weights/IterativeOptEDriver.hhA class for optimizing weights in an iterative weight fitting, sequence recovery test protocol
src/protocols/optimize_weights/NestedEnergyTermOptEData.cc
src/protocols/optimize_weights/NestedEnergyTermOptEData.fwd.hhForward header for some special optE position data classes
src/protocols/optimize_weights/NestedEnergyTermOptEData.hhClasses to store by-energy-term rotamer data for optE, when using the unfolded state energy term
src/protocols/optimize_weights/OptEData.cc
src/protocols/optimize_weights/OptEData.fwd.hhForward declarations for OptE data structures
src/protocols/optimize_weights/OptEData.hh
src/protocols/optimize_weights/OptEMultifunc.cc
src/protocols/optimize_weights/OptEMultifunc.fwd.hh
src/protocols/optimize_weights/OptEMultifunc.hh
src/protocols/optimize_weights/PNatLigPoseOptEData.cc
src/protocols/optimize_weights/PNatLigPoseOptEData.fwd.hh
src/protocols/optimize_weights/PNatLigPoseOptEData.hh
src/protocols/pack_daemon/DynamicAggregateFunction.cc
src/protocols/pack_daemon/DynamicAggregateFunction.fwd.hh
src/protocols/pack_daemon/DynamicAggregateFunction.hhDeclaration for a file-driven definition for the active states in a multistate design and the set of mathematical expressions that together define the fitness function for the sequence being designed
src/protocols/pack_daemon/EntityCorrespondence.ccImplementation for class EntityCorrespondence
src/protocols/pack_daemon/EntityCorrespondence.fwd.hh
src/protocols/pack_daemon/EntityCorrespondence.hhForward declaration for class EntityCorrespondence
src/protocols/pack_daemon/MultistateAggregateFunction.ccImplementation for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class)
src/protocols/pack_daemon/MultistateAggregateFunction.fwd.hhForward declaration of class MultistateAggregateFunction
src/protocols/pack_daemon/MultistateAggregateFunction.hhDeclaration for class MultistateAggregateFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateAggregateFunction class)
src/protocols/pack_daemon/MultistateFitnessFunction.ccImplementation of the class MultistateFitnessFunction
src/protocols/pack_daemon/MultistateFitnessFunction.fwd.hhForward declaration of class MultistateFitnessFunction
src/protocols/pack_daemon/MultistateFitnessFunction.hhDeclaration for class MultistateFitnessFunction to work with the PackDeamon classes (not to be confused with J. Ashworth's MultiStateFitnessFunction class)
src/protocols/pack_daemon/PackDaemon.ccImplementation for class PackDaemon
src/protocols/pack_daemon/PackDaemon.fwd.hh
src/protocols/pack_daemon/PackDaemon.hhDeclaration for class PackDaemon
src/protocols/pmut_scan/Mutant.ccA helper class for the point mut scan protocol which holds data about mutants
src/protocols/pmut_scan/Mutant.fwd.hhForward declaration for Mutant.hh
src/protocols/pmut_scan/Mutant.hhA helper class for the point mut scan protocol
src/protocols/pmut_scan/PointMutScanDriver.ccA protocol that tries to find stability enhancing mutations
src/protocols/pmut_scan/PointMutScanDriver.hh
src/protocols/pockets/Fingerprint.ccProtocols::pockets::Fingerprint functions
src/protocols/pockets/Fingerprint.fwd.hhProtocols::pockets::Fingerprint forward declarations header
src/protocols/pockets/Fingerprint.hhProtocols::pockets::Fingerprint header
src/protocols/pockets/FingerprintMultifunc.cc
src/protocols/pockets/FingerprintMultifunc.fwd.hhProtocols::pockets::FingerprintMultifunc forward declarations
src/protocols/pockets/FingerprintMultifunc.hhFingerprint multifunction class
src/protocols/pockets/PocketConstraint.cc
src/protocols/pockets/PocketConstraint.fwd.hhCore::grid::Pockets::PocketConstraint forward declarations header
src/protocols/pockets/PocketConstraint.hh
src/protocols/pockets/PocketConstraintCreator.hh
src/protocols/pockets/PocketGrid.ccProtocols::pockets::PocketGrid functions
src/protocols/pockets/PocketGrid.fwd.hhProtocols::pockets::PocketGrid forward declarations header
src/protocols/pockets/PocketGrid.hhProtocols::pockets::PocketGrid header
src/protocols/protein_interface_design/design_utils.ccVarious utilities for interface design
src/protocols/protein_interface_design/design_utils.hhDefinition of various classes for interface design
src/protocols/protein_interface_design/dock_design_filter_creators.hhFilterCreators for the filters defined in dock_design_filters.hh
src/protocols/protein_interface_design/dock_design_filters.cc
src/protocols/protein_interface_design/dock_design_filters.hhDefinition of filter classes for iterations of docking/design
src/protocols/protein_interface_design/DockDesignFilterFactory.cc
src/protocols/protein_interface_design/DockDesignFilterFactory.fwd.hh
src/protocols/protein_interface_design/DockDesignFilterFactory.hh
src/protocols/protein_interface_design/parse_filters.cc
src/protocols/protein_interface_design/ParserJobInputter.cc
src/protocols/protein_interface_design/ParserJobInputter.fwd.hh
src/protocols/protein_interface_design/ParserJobInputter.hh
src/protocols/protein_interface_design/ParserJobInputterCreator.hh
src/protocols/protein_interface_design/read_patchdock.cc
src/protocols/protein_interface_design/read_patchdock.hh
src/protocols/protein_interface_design/ReportPSSMDifference.ccCalculation of the difference in PSSM score between mutated and native pose
src/protocols/protein_interface_design/ReportPSSMDifference.fwd.hhCalculation of the difference in PSSM score between mutated and native pose
src/protocols/protein_interface_design/ReportPSSMDifference.hhCalculation of the difference in PSSM score between mutated and native pose
src/protocols/protein_interface_design/util.cc
src/protocols/protein_interface_design/util.hhDefinition of classes for iterations of docking/design
src/protocols/protein_interface_design/filters/AverageDegreeFilter.cc
src/protocols/protein_interface_design/filters/AverageDegreeFilter.fwd.hhForward declaration for AverageDegreeFilter
src/protocols/protein_interface_design/filters/AverageDegreeFilter.hh
src/protocols/protein_interface_design/filters/AverageDegreeFilterCreator.hhFilterCreators for the AverageDegreeFilter
src/protocols/protein_interface_design/filters/BindingStrainFilter.cc
src/protocols/protein_interface_design/filters/BindingStrainFilter.fwd.hhForward declaration for BindingStrainFilter
src/protocols/protein_interface_design/filters/BindingStrainFilter.hh
src/protocols/protein_interface_design/filters/BindingStrainFilterCreator.hhFilterCreators for the BindingStrainFilter
src/protocols/protein_interface_design/filters/BoltzmannFilter.cc
src/protocols/protein_interface_design/filters/BoltzmannFilter.fwd.hhForward declaration for BoltzmannFilter
src/protocols/protein_interface_design/filters/BoltzmannFilter.hh
src/protocols/protein_interface_design/filters/BoltzmannFilterCreator.hhFilterCreators for the BoltzmannFilter
src/protocols/protein_interface_design/filters/DeltaFilter.cc
src/protocols/protein_interface_design/filters/DeltaFilter.fwd.hhForward declaration for DeltaFilter
src/protocols/protein_interface_design/filters/DeltaFilter.hh
src/protocols/protein_interface_design/filters/DeltaFilterCreator.hhFilterCreators for the DeltaFilter
src/protocols/protein_interface_design/filters/DesignableResiduesFilter.cc
src/protocols/protein_interface_design/filters/DesignableResiduesFilter.fwd.hhForward declaration for DesignableResiduesFilter
src/protocols/protein_interface_design/filters/DesignableResiduesFilter.hh
src/protocols/protein_interface_design/filters/DesignableResiduesFilterCreator.hhFilterCreators for the DesignableResiduesFilter
src/protocols/protein_interface_design/filters/DisulfideFilter.cc
src/protocols/protein_interface_design/filters/DisulfideFilter.hhFilters for interfaces which could form a disulfide bond between docking partners
src/protocols/protein_interface_design/filters/DisulfideFilterCreator.hhFilterCreators for the DisulfideFilter
src/protocols/protein_interface_design/filters/FilterScan.cc
src/protocols/protein_interface_design/filters/FilterScan.fwd.hh
src/protocols/protein_interface_design/filters/FilterScan.hh
src/protocols/protein_interface_design/filters/FilterScanCreator.hh
src/protocols/protein_interface_design/filters/HbondsToResidueFilter.cc
src/protocols/protein_interface_design/filters/HbondsToResidueFilter.fwd.hhForward declaration for HbondsToResidueFilter
src/protocols/protein_interface_design/filters/HbondsToResidueFilter.hhDefinition of filter classes for iterations of docking/design
src/protocols/protein_interface_design/filters/HbondsToResidueFilterCreator.hhFilterCreators for the filters defined in HbondsToResidueFilterCreator.hh
src/protocols/protein_interface_design/filters/InterfaceHolesFilter.ccFind packing defects at an interface using packstat score terms
src/protocols/protein_interface_design/filters/InterfaceHolesFilter.hhFind packing defects at an interface using packstat score terms
src/protocols/protein_interface_design/filters/InterfaceHolesFilterCreator.hhFilterCreators for the InterfaceHolesFilter
src/protocols/protein_interface_design/filters/RelativePoseFilter.cc
src/protocols/protein_interface_design/filters/RelativePoseFilter.fwd.hhForward declaration for RelativePoseFilter
src/protocols/protein_interface_design/filters/RelativePoseFilter.hh
src/protocols/protein_interface_design/filters/RelativePoseFilterCreator.hhFilterCreators for the RelativePoseFilter
src/protocols/protein_interface_design/filters/RelativeSegmentFilter.cc
src/protocols/protein_interface_design/filters/RelativeSegmentFilter.fwd.hhForward declaration for RelativeSegmentFilter
src/protocols/protein_interface_design/filters/RelativeSegmentFilter.hh
src/protocols/protein_interface_design/filters/RelativeSegmentFilterCreator.hhFilterCreators for the filters defined in RelativeSegmentFilterCreator.hh
src/protocols/protein_interface_design/filters/RmsdFilter.ccRmsd filtering
src/protocols/protein_interface_design/filters/RmsdFilter.hhFind packing defects at an interface using packstat score terms
src/protocols/protein_interface_design/filters/RmsdFilterCreator.hhFilterCreators for the RmsdFilter
src/protocols/protein_interface_design/filters/SequenceRecoveryFilter.cc
src/protocols/protein_interface_design/filters/SequenceRecoveryFilter.fwd.hhForward declaration for SequenceRecoveryFilter
src/protocols/protein_interface_design/filters/SequenceRecoveryFilter.hh
src/protocols/protein_interface_design/filters/SequenceRecoveryFilterCreator.hhFilterCreators for the SequenceRecoveryFilter
src/protocols/protein_interface_design/filters/StubScoreFilter.cc
src/protocols/protein_interface_design/filters/StubScoreFilter.fwd.hhForward declaration for StubScoreFilter
src/protocols/protein_interface_design/filters/StubScoreFilter.hh
src/protocols/protein_interface_design/filters/StubScoreFilterCreator.hhFilterCreators for the StubScoreFilter
src/protocols/protein_interface_design/filters/TorsionFilter.cc
src/protocols/protein_interface_design/filters/TorsionFilter.fwd.hh
src/protocols/protein_interface_design/filters/TorsionFilter.hh
src/protocols/protein_interface_design/filters/TorsionFilterCreator.hh
src/protocols/protein_interface_design/movers/AddChainBreak.cc
src/protocols/protein_interface_design/movers/AddChainBreak.hh
src/protocols/protein_interface_design/movers/AddChainBreakCreator.hhDeclaration of the MoverCreator class for the AddChainBreak
src/protocols/protein_interface_design/movers/AddSidechainConstraintsToHotspots.cc
src/protocols/protein_interface_design/movers/AddSidechainConstraintsToHotspots.hh
src/protocols/protein_interface_design/movers/AddSidechainConstraintsToHotspotsCreator.hhDeclaration of the MoverCreator class for the AddSidechainConstraintsToHotspots
src/protocols/protein_interface_design/movers/BackrubDDMover.cc
src/protocols/protein_interface_design/movers/BackrubDDMover.hhDerived class from mover for dock design with backrub moves
src/protocols/protein_interface_design/movers/BackrubDDMoverCreator.hhDeclaration of the MoverCreator class for the BackrubDDMover
src/protocols/protein_interface_design/movers/BestHotspotCstMover.cc
src/protocols/protein_interface_design/movers/BestHotspotCstMover.hh
src/protocols/protein_interface_design/movers/BestHotspotCstMoverCreator.hhDeclaration of the MoverCreator class for the BestHotspotCstMover
src/protocols/protein_interface_design/movers/BuildAlaPose.cc
src/protocols/protein_interface_design/movers/BuildAlaPose.fwd.hh
src/protocols/protein_interface_design/movers/BuildAlaPose.hh
src/protocols/protein_interface_design/movers/BuildAlaPoseCreator.hhDeclaration of the MoverCreator class for the BuildAlaPose
src/protocols/protein_interface_design/movers/DesignMinimizeHbonds.cc
src/protocols/protein_interface_design/movers/DesignMinimizeHbonds.hh
src/protocols/protein_interface_design/movers/DesignMinimizeHbondsCreator.hhDeclaration of the MoverCreator class for the DesignMinimizeHbonds
src/protocols/protein_interface_design/movers/DisulfideMover.cc
src/protocols/protein_interface_design/movers/DisulfideMover.hh
src/protocols/protein_interface_design/movers/DisulfideMoverCreator.hhDeclaration of the MoverCreator class for the DisulfideMover
src/protocols/protein_interface_design/movers/DockAndRetrieveSidechains.cc
src/protocols/protein_interface_design/movers/DockAndRetrieveSidechains.hh
src/protocols/protein_interface_design/movers/DockAndRetrieveSidechainsCreator.hhDeclaration of the MoverCreator class for the DockAndRetrieveSidechains
src/protocols/protein_interface_design/movers/DumpPdb.cc
src/protocols/protein_interface_design/movers/DumpPdb.hh
src/protocols/protein_interface_design/movers/DumpPdbCreator.hhDeclaration of the MoverCreator class for the DumpPdb
src/protocols/protein_interface_design/movers/FavorNativeResiduePreCycle.cc
src/protocols/protein_interface_design/movers/FavorNativeResiduePreCycle.hh
src/protocols/protein_interface_design/movers/FavorNativeResiduePreCycleCreator.hhDeclaration of the MoverCreator class for the FavorNativeResiduePreCycle
src/protocols/protein_interface_design/movers/FavorNonNativeResiduePreCycle.cc
src/protocols/protein_interface_design/movers/FavorNonNativeResiduePreCycle.hh
src/protocols/protein_interface_design/movers/FavorNonNativeResiduePreCycleCreator.hh
src/protocols/protein_interface_design/movers/HotspotDisjointedFoldTreeMover.cc
src/protocols/protein_interface_design/movers/HotspotDisjointedFoldTreeMover.hh
src/protocols/protein_interface_design/movers/HotspotDisjointedFoldTreeMoverCreator.hhDeclaration of the MoverCreator class for the HotspotDisjointedFoldTreeMover
src/protocols/protein_interface_design/movers/HotspotHasherMover.cc
src/protocols/protein_interface_design/movers/HotspotHasherMover.hh
src/protocols/protein_interface_design/movers/HotspotHasherMoverCreator.hhDeclaration of the MoverCreator class for the HotspotHasherMover
src/protocols/protein_interface_design/movers/InterfaceRecapitulationMover.cc
src/protocols/protein_interface_design/movers/InterfaceRecapitulationMover.hh
src/protocols/protein_interface_design/movers/InterfaceRecapitulationMoverCreator.hhDeclaration of the MoverCreator class for the InterfaceRecapitulationMover
src/protocols/protein_interface_design/movers/LoopFinder.cc
src/protocols/protein_interface_design/movers/LoopFinder.hhHeader for class to find loops (parseable options to control how loops are found)
src/protocols/protein_interface_design/movers/LoopFinderCreator.hhDeclaration of the MoverCreator class for the LoopFinder
src/protocols/protein_interface_design/movers/LoopLengthChange.cc
src/protocols/protein_interface_design/movers/LoopLengthChange.fwd.hh
src/protocols/protein_interface_design/movers/LoopLengthChange.hh
src/protocols/protein_interface_design/movers/LoopLengthChangeCreator.hhDeclaration of the MoverCreator class for the LoopLengthChange
src/protocols/protein_interface_design/movers/LoopMoverFromCommandLine.cc
src/protocols/protein_interface_design/movers/LoopMoverFromCommandLine.fwd.hh
src/protocols/protein_interface_design/movers/LoopMoverFromCommandLine.hh
src/protocols/protein_interface_design/movers/LoopMoverFromCommandLineCreator.hh
src/protocols/protein_interface_design/movers/LoopOver.cc
src/protocols/protein_interface_design/movers/LoopOver.hh
src/protocols/protein_interface_design/movers/LoopOverCreator.hhDeclaration of the MoverCreator class for the LoopOver
src/protocols/protein_interface_design/movers/LoopRemodel.ccParseable class to run loop perturbation or refinement between a given loop between start/end (inclusive). Intended to sample loop conformations at an interface
src/protocols/protein_interface_design/movers/LoopRemodel.fwd.hh
src/protocols/protein_interface_design/movers/LoopRemodel.hhHeader for parseable class to run loop perturbation or refinement between a given loop between start/end (inclusive)
src/protocols/protein_interface_design/movers/LoopRemodelCreator.hhDeclaration of the MoverCreator class for the LoopRemodel
src/protocols/protein_interface_design/movers/MapHotspot.cc
src/protocols/protein_interface_design/movers/MapHotspot.hh
src/protocols/protein_interface_design/movers/MapHotspotCreator.hhDeclaration of the MoverCreator class for the MapHotspot
src/protocols/protein_interface_design/movers/NullDesignMover.cc
src/protocols/protein_interface_design/movers/NullDesignMover.hh
src/protocols/protein_interface_design/movers/PeptideStapleDesignMover.cc
src/protocols/protein_interface_design/movers/PeptideStapleDesignMover.hh
src/protocols/protein_interface_design/movers/PeptideStapleDesignMoverCreator.hhDeclaration of the MoverCreator class for the PeptideStapleDesignMover
src/protocols/protein_interface_design/movers/PlacementAuctionMover.cc
src/protocols/protein_interface_design/movers/PlacementAuctionMover.fwd.hhForward declations for PlacementAuctionMover
src/protocols/protein_interface_design/movers/PlacementAuctionMover.hhDefinition of a class for making the placement auction used by PlaceSimultaneouslyMover
src/protocols/protein_interface_design/movers/PlacementAuctionMoverCreator.hhDeclaration of the MoverCreator class for the PlacementAuctionMover
src/protocols/protein_interface_design/movers/PlacementMinimizationMover.cc
src/protocols/protein_interface_design/movers/PlacementMinimizationMover.fwd.hhForward declations for PlacementMinimizationMover
src/protocols/protein_interface_design/movers/PlacementMinimizationMover.hhDefinition of a class for making the placement auction used by PlaceSimultaneouslyMover
src/protocols/protein_interface_design/movers/PlacementMinimizationMoverCreator.hhDeclaration of the MoverCreator class for the PlacementMinimizationMover
src/protocols/protein_interface_design/movers/PlaceOnLoop.cc
src/protocols/protein_interface_design/movers/PlaceOnLoop.fwd.hh
src/protocols/protein_interface_design/movers/PlaceOnLoop.hh
src/protocols/protein_interface_design/movers/PlaceOnLoopCreator.hhDeclaration of the MoverCreator class for the PlaceOnLoop
src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.cc
src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.hh
src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMoverCreator.hhDeclaration of the MoverCreator class for the PlaceSimultaneouslyMover
src/protocols/protein_interface_design/movers/PlaceStubMover.cc
src/protocols/protein_interface_design/movers/PlaceStubMover.fwd.hhForward declarations for PlaceStubMover
src/protocols/protein_interface_design/movers/PlaceStubMover.hhDefinition of classes for grafting hotspots into a pose
src/protocols/protein_interface_design/movers/PlaceStubMoverCreator.hhDeclaration of the MoverCreator class for the PlaceStubMover
src/protocols/protein_interface_design/movers/PlaceUtils.ccCollection of utility functions for placement classes
src/protocols/protein_interface_design/movers/PlaceUtils.hh
src/protocols/protein_interface_design/movers/PrepackMover.cc
src/protocols/protein_interface_design/movers/PrepackMover.hh
src/protocols/protein_interface_design/movers/PrepackMoverCreator.hhDeclaration of the MoverCreator class for the PrepackMover
src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.cc
src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.fwd.hh
src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.hh
src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMoverCreator.hhDeclaration of the MoverCreator class for the ProteinInterfaceMultiStateDesignMover
src/protocols/protein_interface_design/movers/RandomMutation.cc
src/protocols/protein_interface_design/movers/RandomMutation.fwd.hh
src/protocols/protein_interface_design/movers/RandomMutation.hh
src/protocols/protein_interface_design/movers/RandomMutationCreator.hhDeclaration of the MoverCreator class for the RandomMutation
src/protocols/protein_interface_design/movers/RepackMinimize.cc
src/protocols/protein_interface_design/movers/RepackMinimize.hh
src/protocols/protein_interface_design/movers/RepackMinimizeCreator.hhDeclaration of the MoverCreator class for the RepackMinimize
src/protocols/protein_interface_design/movers/SaveAndRetrieveSidechains.cc
src/protocols/protein_interface_design/movers/SaveAndRetrieveSidechains.fwd.hh
src/protocols/protein_interface_design/movers/SaveAndRetrieveSidechains.hh
src/protocols/protein_interface_design/movers/SaveAndRetrieveSidechainsCreator.hhDeclaration of the MoverCreator class for the SaveAndRetrieveSidechains
src/protocols/protein_interface_design/movers/SetAtomTree.cc
src/protocols/protein_interface_design/movers/SetAtomTree.hh
src/protocols/protein_interface_design/movers/SetAtomTreeCreator.hhDeclaration of the MoverCreator class for the SetAtomTree
src/protocols/protein_interface_design/movers/SetTemperatureFactor.cc
src/protocols/protein_interface_design/movers/SetTemperatureFactor.fwd.hh
src/protocols/protein_interface_design/movers/SetTemperatureFactor.hh
src/protocols/protein_interface_design/movers/SetTemperatureFactorCreator.hhDeclaration of the MoverCreator class for the SetTemperatureFactor
src/protocols/protein_interface_design/movers/SetupHotspotConstraintsMover.cc
src/protocols/protein_interface_design/movers/SetupHotspotConstraintsMover.hhDerived classes from DockDesign for dock design
src/protocols/protein_interface_design/movers/SetupHotspotConstraintsMoverCreator.hhDeclaration of the MoverCreator class for the SetupHotspotConstraintsMover
src/protocols/protein_interface_design/movers/SpinMover.cc
src/protocols/protein_interface_design/movers/SpinMover.hh
src/protocols/protein_interface_design/movers/SpinMoverCreator.hhDeclaration of the MoverCreator class for the SpinMover
src/protocols/protein_interface_design/movers/SubroutineMover.cc
src/protocols/protein_interface_design/movers/SubroutineMover.fwd.hhForward declations for SubroutineMover
src/protocols/protein_interface_design/movers/SubroutineMover.hhDefinition of a class for making the placement auction used by PlaceSimultaneouslyMover
src/protocols/protein_interface_design/movers/SubroutineMoverCreator.hhDeclaration of the MoverCreator class for the SubroutineMover
src/protocols/protein_interface_design/movers/TaskAwareCsts.cc
src/protocols/protein_interface_design/movers/TaskAwareCsts.fwd.hh
src/protocols/protein_interface_design/movers/TaskAwareCsts.hh
src/protocols/protein_interface_design/movers/TaskAwareCstsCreator.hhDeclaration of the MoverCreator class for the TaskAwareCsts
src/protocols/protein_interface_design/movers/TryRotamers.cc
src/protocols/protein_interface_design/movers/TryRotamers.hh
src/protocols/protein_interface_design/movers/TryRotamersCreator.hhDeclaration of the MoverCreator class for the TryRotamers
src/protocols/protein_interface_design/movers/VLB.cc
src/protocols/protein_interface_design/movers/VLB.hh
src/protocols/protein_interface_design/movers/VLBCreator.hhDeclaration of the MoverCreator class for the VLB
src/protocols/qsar/qsarMap.cc
src/protocols/qsar/qsarMap.fwd.hh
src/protocols/qsar/qsarMap.hh
src/protocols/qsar/qsarMover.cc
src/protocols/qsar/qsarMover.fwd.hh
src/protocols/qsar/qsarMover.hh
src/protocols/qsar/qsarMoverCreator.hh
src/protocols/qsar/qsarOptFunc.cc
src/protocols/qsar/qsarOptFunc.fwd.hh
src/protocols/qsar/qsarOptFunc.hh
src/protocols/qsar/RenderGridsToKinemage.cc
src/protocols/qsar/RenderGridsToKinemage.fwd.hh
src/protocols/qsar/RenderGridsToKinemage.hh
src/protocols/qsar/RenderGridsToKinemageCreator.hh
src/protocols/qsar/scoring_grid/AtrGrid.cc
src/protocols/qsar/scoring_grid/AtrGrid.fwd.hh
src/protocols/qsar/scoring_grid/AtrGrid.hh
src/protocols/qsar/scoring_grid/AtrGridCreator.hh
src/protocols/qsar/scoring_grid/ClassicGrid.cc
src/protocols/qsar/scoring_grid/ClassicGrid.fwd.hh
src/protocols/qsar/scoring_grid/ClassicGrid.hh
src/protocols/qsar/scoring_grid/ClassicGridCreator.hh
src/protocols/qsar/scoring_grid/GridBase.cc
src/protocols/qsar/scoring_grid/GridBase.fwd.hh
src/protocols/qsar/scoring_grid/GridBase.hh
src/protocols/qsar/scoring_grid/GridCreator.cc
src/protocols/qsar/scoring_grid/GridCreator.hhBase class for GridCreators for the Grid load time factory registration scheme
src/protocols/qsar/scoring_grid/GridFactory.cc
src/protocols/qsar/scoring_grid/GridFactory.fwd.hh
src/protocols/qsar/scoring_grid/GridFactory.hh
src/protocols/qsar/scoring_grid/GridManager.cc
src/protocols/qsar/scoring_grid/GridManager.fwd.hh
src/protocols/qsar/scoring_grid/GridManager.hh
src/protocols/qsar/scoring_grid/HbaGrid.cc
src/protocols/qsar/scoring_grid/HbaGrid.fwd.hh
src/protocols/qsar/scoring_grid/HbaGrid.hh
src/protocols/qsar/scoring_grid/HbaGridCreator.hh
src/protocols/qsar/scoring_grid/HbdGrid.cc
src/protocols/qsar/scoring_grid/HbdGrid.fwd.hh
src/protocols/qsar/scoring_grid/HbdGrid.hh
src/protocols/qsar/scoring_grid/HbdGridCreator.hh
src/protocols/qsar/scoring_grid/polarizGrid.cc
src/protocols/qsar/scoring_grid/polarizGrid.fwd.hh
src/protocols/qsar/scoring_grid/polarizGrid.hh
src/protocols/qsar/scoring_grid/polarizGridCreator.hh
src/protocols/qsar/scoring_grid/RepGrid.cc
src/protocols/qsar/scoring_grid/RepGrid.fwd.hh
src/protocols/qsar/scoring_grid/RepGrid.hh
src/protocols/qsar/scoring_grid/RepGridCreator.hh
src/protocols/qsar/scoring_grid/ScoringGridLoader.cc
src/protocols/qsar/scoring_grid/ScoringGridLoader.fwd.hh
src/protocols/qsar/scoring_grid/ScoringGridLoader.hh
src/protocols/qsar/scoring_grid/ScoringGridLoaderCreator.hh
src/protocols/qsar/scoring_grid/VdwGrid.cc
src/protocols/qsar/scoring_grid/VdwGrid.fwd.hh
src/protocols/qsar/scoring_grid/VdwGrid.hh
src/protocols/qsar/scoring_grid/VdwGridCreator.hh
src/protocols/rbsegment_relax/AutoRBRelaxMover.cc
src/protocols/rbsegment_relax/AutoRBRelaxMover.hh
src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc
src/protocols/rbsegment_relax/FragInsertAndAlignMover.hh
src/protocols/rbsegment_relax/RBSegment.cc
src/protocols/rbsegment_relax/RBSegment.fwd.hh
src/protocols/rbsegment_relax/RBSegment.hh
src/protocols/rbsegment_relax/RBSegmentMover.cc
src/protocols/rbsegment_relax/RBSegmentMover.hh
src/protocols/rbsegment_relax/RBSegmentRelax.ccRBSegmentRelax protocol
src/protocols/rbsegment_relax/RBSegmentRelax.hhRBSegmentRelax protocol
src/protocols/rbsegment_relax/RBSegmentRelax_main.cc
src/protocols/rbsegment_relax/RBSegmentRelax_main.hh
src/protocols/rbsegment_relax/util.cc
src/protocols/rbsegment_relax/util.hh
src/protocols/relax/ClassicRelax.cc
src/protocols/relax/ClassicRelax.hh
src/protocols/relax/cst_util.cc
src/protocols/relax/cst_util.hhSet of functions for adding constraints used in relax
src/protocols/relax/FastRelax.ccThe FastRelax Protocol
src/protocols/relax/FastRelax.fwd.hh
src/protocols/relax/FastRelax.hhThe FastRelax Protocol
src/protocols/relax/FastRelaxCreator.hh
src/protocols/relax/MiniRelax.cc
src/protocols/relax/MiniRelax.fwd.hhForward declaration for MiniRelax class
src/protocols/relax/MiniRelax.hh
src/protocols/relax/Ramady.ccHeader for the Rana energy repair code, Ramady
src/protocols/relax/Ramady.hhHeader for the Rana energy repair code, Ramady
src/protocols/relax/relax_main.cc
src/protocols/relax/relax_main.hh
src/protocols/relax/RelaxProtocolBase.cc
src/protocols/relax/RelaxProtocolBase.fwd.hh
src/protocols/relax/RelaxProtocolBase.hh
src/protocols/relax/util.cc
src/protocols/relax/util.hh
src/protocols/relax/WorkUnit_BatchRelax.cc
src/protocols/relax/WorkUnit_BatchRelax.hh
src/protocols/rigid/PoseMembraneRigidBodyMover.cc
src/protocols/rigid/PoseMembraneRigidBodyMover.hh
src/protocols/rigid/RB_geometry.cc
src/protocols/rigid/RB_geometry.hh
src/protocols/rigid/rigid_body_moves.cc
src/protocols/rigid/rigid_body_moves.hh
src/protocols/rigid/RigidBodyMotionMover.cc
src/protocols/rigid/RigidBodyMotionMover.fwd.hh
src/protocols/rigid/RigidBodyMotionMover.hh
src/protocols/rigid/RigidBodyMover.cc
src/protocols/rigid/RigidBodyMover.fwd.hhRigidBodyMover forward declarations header
src/protocols/rigid/RigidBodyMover.hh
src/protocols/rigid/RigidBodyMoverCreator.hhThis class will create instances of Movers SmallMover and ShearMover for the MoverFactory
src/protocols/rigid/RollMover.cc
src/protocols/rigid/RollMover.fwd.hhRollMover forward declarations header
src/protocols/rigid/RollMover.hh
src/protocols/rigid/RollMoverCreator.hhThis class will create instances of Mover RollMover for the MoverFactory
src/protocols/rigid/RotateJumpAxisMover.ccRotateJumpAxisMover methods implemented
src/protocols/rigid/RotateJumpAxisMover.fwd.hhRotateJumpAxisMover forward declarations header
src/protocols/rigid/RotateJumpAxisMover.hhRotateJumpAxisMover header
src/protocols/rna/FullAtomRNA_Fragments.cc
src/protocols/rna/FullAtomRNA_Fragments.fwd.hh
src/protocols/rna/FullAtomRNA_Fragments.hh
src/protocols/rna/MultipleDomainMover.cc
src/protocols/rna/MultipleDomainMover.fwd.hhForward declarations header
src/protocols/rna/MultipleDomainMover.hh
src/protocols/rna/RNA_BasePairClassifier.cc
src/protocols/rna/RNA_BasePairClassifier.hh
src/protocols/rna/RNA_ChunkLibrary.cc
src/protocols/rna/RNA_ChunkLibrary.fwd.hh
src/protocols/rna/RNA_ChunkLibrary.hhForward declarations header
src/protocols/rna/RNA_DataReader.cc
src/protocols/rna/RNA_DataReader.fwd.hh
src/protocols/rna/RNA_DataReader.hh
src/protocols/rna/RNA_DeNovoProtocol.cc
src/protocols/rna/RNA_DeNovoProtocol.hh
src/protocols/rna/RNA_FragmentMover.cc
src/protocols/rna/RNA_FragmentMover.fwd.hh
src/protocols/rna/RNA_FragmentMover.hh
src/protocols/rna/RNA_Fragments.cc
src/protocols/rna/RNA_Fragments.fwd.hh
src/protocols/rna/RNA_Fragments.hh
src/protocols/rna/rna_fragments_classes.fwd.hh
src/protocols/rna/RNA_FragmentsClasses.cc
src/protocols/rna/RNA_FragmentsClasses.fwd.hh
src/protocols/rna/RNA_FragmentsClasses.hh
src/protocols/rna/RNA_HelixAssembler.cc
src/protocols/rna/RNA_HelixAssembler.fwd.hh
src/protocols/rna/RNA_HelixAssembler.hh
src/protocols/rna/RNA_JumpLibrary.cc
src/protocols/rna/RNA_JumpLibrary.fwd.hh
src/protocols/rna/RNA_JumpLibrary.hh
src/protocols/rna/RNA_LoopCloser.cc
src/protocols/rna/RNA_LoopCloser.fwd.hh
src/protocols/rna/RNA_LoopCloser.hh
src/protocols/rna/RNA_MatchType.hh
src/protocols/rna/RNA_Minimizer.cc
src/protocols/rna/RNA_Minimizer.fwd.hh
src/protocols/rna/RNA_Minimizer.hh
src/protocols/rna/RNA_ProtocolUtil.cc
src/protocols/rna/RNA_ProtocolUtil.hh
src/protocols/rna/RNA_Relaxer.cc
src/protocols/rna/RNA_Relaxer.fwd.hh
src/protocols/rna/RNA_Relaxer.hh
src/protocols/rna/RNA_SecStructInfo.cc
src/protocols/rna/RNA_SecStructInfo.fwd.hh
src/protocols/rna/RNA_SecStructInfo.hh
src/protocols/rna/RNA_StructureParameters.cc
src/protocols/rna/RNA_StructureParameters.fwd.hh
src/protocols/rna/RNA_StructureParameters.hh
src/protocols/rosetta_scripts/ParsedProtocol.cc
src/protocols/rosetta_scripts/ParsedProtocol.fwd.hhForward declarations for ParsedProtocol
src/protocols/rosetta_scripts/ParsedProtocol.hh
src/protocols/rosetta_scripts/ParsedProtocolCreator.hhThis class will create instances of Mover DockDesign for the MoverFactory
src/protocols/rosetta_scripts/SavePoseMover.cc
src/protocols/rosetta_scripts/SavePoseMover.fwd.hh
src/protocols/rosetta_scripts/SavePoseMover.hh
src/protocols/rosetta_scripts/SavePoseMoverCreator.hhThis class will create instances of Mover SavePoseMover for the MoverFactory
src/protocols/rosetta_scripts/util.cc
src/protocols/rosetta_scripts/util.hh
src/protocols/rotamer_recovery/RotamerRecovery.cc
src/protocols/rotamer_recovery/RotamerRecovery.fwd.hhMeasure how well rosetta is a recovering the conformation of an experimentally validated structure
src/protocols/rotamer_recovery/RotamerRecovery.hh
src/protocols/rotamer_recovery/RotamerRecoveryCreator.ccCreator classes for components of the RotamerRecovery framework
src/protocols/rotamer_recovery/RotamerRecoveryCreator.fwd.hh
src/protocols/rotamer_recovery/RotamerRecoveryCreator.hh
src/protocols/rotamer_recovery/RotamerRecoveryFactory.ccFactory for creating RotamerRecoverys objects
src/protocols/rotamer_recovery/RotamerRecoveryFactory.fwd.hhReport atom-atom pair geometry and scores to rotamer_recovery Statistics Scientific Benchmark
src/protocols/rotamer_recovery/RotamerRecoveryFactory.hhFactory for creating RotamerRecovery objects
src/protocols/rotamer_recovery/RotamerRecoveryMover.ccA wrapper that measures how similar the rotamers are between before and after running the child mover
src/protocols/rotamer_recovery/RotamerRecoveryMover.fwd.hhMeasure how well rosetta is a recovering the conformation of an experimentally validated structure
src/protocols/rotamer_recovery/RotamerRecoveryMover.hhA wrapper that measures how similar the rotamers are between before and after running the child mover
src/protocols/rotamer_recovery/RotamerRecoveryMoverCreator.hhThis class will create instances of Mover ConstraintSetMover for the MoverFactory
src/protocols/rotamer_recovery/RRComparer.cc
src/protocols/rotamer_recovery/RRComparer.fwd.hhMeasure how well rosetta is a recovering the conformation of an experimentally validated structure
src/protocols/rotamer_recovery/RRComparer.hh
src/protocols/rotamer_recovery/RRComparerAutomorphicRMSD.cc
src/protocols/rotamer_recovery/RRComparerAutomorphicRMSD.fwd.hhMeasure how well rosetta is a recovering the conformation of an experimentally validated structure by measuing the minimum root mean squared deviation of sidechain atoms for all chemical atomorphic forms
src/protocols/rotamer_recovery/RRComparerAutomorphicRMSD.hh
src/protocols/rotamer_recovery/RRProtocol.cc
src/protocols/rotamer_recovery/RRProtocol.fwd.hhManage how the rotamer recovery test should be preformed
src/protocols/rotamer_recovery/RRProtocol.hh
src/protocols/rotamer_recovery/RRProtocolMinPack.cc
src/protocols/rotamer_recovery/RRProtocolMinPack.fwd.hhPreform the rotamer recovery test by minimizing each residue in a fixed context
src/protocols/rotamer_recovery/RRProtocolMinPack.hh
src/protocols/rotamer_recovery/RRProtocolMover.ccPreform the rotamer recovery after applying mover
src/protocols/rotamer_recovery/RRProtocolMover.fwd.hhPreform the rotamer recovery after applying mover
src/protocols/rotamer_recovery/RRProtocolMover.hhPreform the rotamer recovery after applying mover
src/protocols/rotamer_recovery/RRProtocolReferenceStructure.ccPreform the rotamer recovery against a reference structure
src/protocols/rotamer_recovery/RRProtocolReferenceStructure.fwd.hhPreform the rotamer recovery after applying mover
src/protocols/rotamer_recovery/RRProtocolReferenceStructure.hhPreform the rotamer recovery against a reference structure
src/protocols/rotamer_recovery/RRProtocolRTMin.cc
src/protocols/rotamer_recovery/RRProtocolRTMin.fwd.hhPreform the rotamer recovery test by minimizing each residue in a fixed context
src/protocols/rotamer_recovery/RRProtocolRTMin.hh
src/protocols/rotamer_recovery/RRReporter.cc
src/protocols/rotamer_recovery/RRReporter.fwd.hh
src/protocols/rotamer_recovery/RRReporter.hh
src/protocols/rotamer_recovery/RRReporterHuman.cc
src/protocols/rotamer_recovery/RRReporterHuman.fwd.hhReport how well rosetta is a recovering the conformation of an experimentally validated structure in a human readable format
src/protocols/rotamer_recovery/RRReporterHuman.hh
src/protocols/rotamer_recovery/RRReporterSQLite.cc
src/protocols/rotamer_recovery/RRReporterSQLite.fwd.hhReport Rotamer Recovery to an SQLite database
src/protocols/rotamer_recovery/RRReporterSQLite.hh
src/protocols/RotamerDump/RotamerDumpMover.cc
src/protocols/RotamerDump/RotamerDumpMover.fwd.hh
src/protocols/RotamerDump/RotamerDumpMover.hh
src/protocols/scoring/ImplicitFastClashCheck.cc
src/protocols/scoring/ImplicitFastClashCheck.fwd.hh
src/protocols/scoring/ImplicitFastClashCheck.hh
src/protocols/scoring/InterchainPotential.ccStatistically derived rotamer pair potentials
src/protocols/scoring/InterchainPotential.fwd.hh
src/protocols/scoring/InterchainPotential.hh
src/protocols/scoring/Interface.cc
src/protocols/scoring/Interface.fwd.hh
src/protocols/scoring/Interface.hh
src/protocols/scoring/InterfaceInfo.ccStatistically derived rotamer pair potentials
src/protocols/scoring/InterfaceInfo.fwd.hh
src/protocols/scoring/InterfaceInfo.hh
src/protocols/scoring/ResidualDipolarCouplingRigidSegments.cc
src/protocols/scoring/ResidualDipolarCouplingRigidSegments.fwd.hh
src/protocols/scoring/ResidualDipolarCouplingRigidSegments.hh
src/protocols/scoring/methods/EnsembleEnergy.ccFunction to subtract out individual reference energies during ensemble docking
src/protocols/scoring/methods/EnsembleEnergy.hh
src/protocols/scoring/methods/EnsembleEnergyCreator.hhDeclaration for the class that connects EnsembleEnergy with the ScoringManager
src/protocols/scoring/methods/InterchainEnergy.fwd.hh
src/protocols/scoring/methods/InterchainEnvEnergy.ccStatistically derived rotamer pair potentials
src/protocols/scoring/methods/InterchainEnvEnergy.hh
src/protocols/scoring/methods/InterchainEnvEnergyCreator.hhDeclaration for the class that connects InterchainEnvEnergy with the ScoringManager
src/protocols/scoring/methods/InterchainPairEnergy.cc
src/protocols/scoring/methods/InterchainPairEnergy.hh
src/protocols/scoring/methods/InterchainPairEnergyCreator.hh
src/protocols/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.cc
src/protocols/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.fwd.hh
src/protocols/scoring/methods/ResidualDipolarCouplingEnergyRigidSegments.hh
src/protocols/scoring/methods/ResidualDipolarCouplingEnergyRigidSegmentsCreator.hh
src/protocols/scoring/methods/SpecialRotamerEnergy.cc
src/protocols/scoring/methods/SpecialRotamerEnergy.fwd.hh
src/protocols/scoring/methods/SpecialRotamerEnergy.hhAdds a bonus to any rotamer that is flagged
src/protocols/scoring/methods/SpecialRotamerEnergyCreator.hhDeclaration for the class that connects SpecialRotamerEnergy with the ScoringManager
src/protocols/scoring/methods/pcs/GridSearchIterator.cc
src/protocols/scoring/methods/pcs/GridSearchIterator.fwd.hh
src/protocols/scoring/methods/pcs/GridSearchIterator.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftData.ccHold the PCS data on which the SVD will be applied
src/protocols/scoring/methods/pcs/PseudocontactShiftData.fwd.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftData.hhHold the PCS data on which the SVD will be applyed
src/protocols/scoring/methods/pcs/PseudocontactShiftEnergy.cc
src/protocols/scoring/methods/pcs/PseudocontactShiftEnergy.fwd.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftEnergy.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftEnergyCreator.hhDeclaration for the class that connects PseudocontactShiftEnergy with the ScoringManager
src/protocols/scoring/methods/pcs/PseudocontactShiftInput.cc
src/protocols/scoring/methods/pcs/PseudocontactShiftInput.fwd.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftInput.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftTensor.cc
src/protocols/scoring/methods/pcs/PseudocontactShiftTensor.fwd.hh
src/protocols/scoring/methods/pcs/PseudocontactShiftTensor.hh
src/protocols/scoring/methods/pcs/TensorsOptimizer.cc
src/protocols/scoring/methods/pcs/TensorsOptimizer.fwd.hh
src/protocols/scoring/methods/pcs/TensorsOptimizer.hh
src/protocols/scoring/methods/pcs2/GridSearchIterator.cc
src/protocols/scoring/methods/pcs2/GridSearchIterator.fwd.hh
src/protocols/scoring/methods/pcs2/GridSearchIterator.hh
src/protocols/scoring/methods/pcs2/GridSearchIteratorCA.cc
src/protocols/scoring/methods/pcs2/GridSearchIteratorCA.fwd.hh
src/protocols/scoring/methods/pcs2/GridSearchIteratorCA.hh
src/protocols/scoring/methods/pcs2/PcsDataCenter.cc
src/protocols/scoring/methods/pcs2/PcsDataCenter.fwd.hh
src/protocols/scoring/methods/pcs2/PcsDataCenter.hhHold the PCS data on which the SVD will be applyed
src/protocols/scoring/methods/pcs2/PcsDataCenterManager.cc
src/protocols/scoring/methods/pcs2/PcsDataCenterManager.fwd.hh
src/protocols/scoring/methods/pcs2/PcsDataCenterManager.hh
src/protocols/scoring/methods/pcs2/PcsDataCenterManagerSingleton.cc
src/protocols/scoring/methods/pcs2/PcsDataCenterManagerSingleton.fwd.hh
src/protocols/scoring/methods/pcs2/PcsDataCenterManagerSingleton.hh
src/protocols/scoring/methods/pcs2/PcsDataLanthanide.cc
src/protocols/scoring/methods/pcs2/PcsDataLanthanide.fwd.hh
src/protocols/scoring/methods/pcs2/PcsDataLanthanide.hh
src/protocols/scoring/methods/pcs2/PcsEnergy.cc
src/protocols/scoring/methods/pcs2/PcsEnergy.fwd.hh
src/protocols/scoring/methods/pcs2/PcsEnergy.hh
src/protocols/scoring/methods/pcs2/PcsEnergyCreator.hhDeclaration for the class that connects PcsEnergyCreator with the ScoringManager
src/protocols/scoring/methods/pcs2/PcsEnergyParameter.cc
src/protocols/scoring/methods/pcs2/PcsEnergyParameter.fwd.hh
src/protocols/scoring/methods/pcs2/PcsEnergyParameter.hh
src/protocols/scoring/methods/pcs2/PcsEnergyParameterManager.cc
src/protocols/scoring/methods/pcs2/PcsEnergyParameterManager.fwd.hh
src/protocols/scoring/methods/pcs2/PcsEnergyParameterManager.hh
src/protocols/scoring/methods/pcs2/PcsGridSearchParameter.cc
src/protocols/scoring/methods/pcs2/PcsGridSearchParameter.fwd.hh
src/protocols/scoring/methods/pcs2/PcsGridSearchParameter.hh
src/protocols/scoring/methods/pcs2/PcsGridSearchParameterManager.cc
src/protocols/scoring/methods/pcs2/PcsGridSearchParameterManager.fwd.hh
src/protocols/scoring/methods/pcs2/PcsGridSearchParameterManager.hh
src/protocols/scoring/methods/pcs2/PcsInputCenter.cc
src/protocols/scoring/methods/pcs2/PcsInputCenter.fwd.hhChristophe Schmitz
src/protocols/scoring/methods/pcs2/PcsInputCenter.hhThis class hold the information for each paramagnetic center Multiple data set with different lanthanide can be measured for each paramagnetic center
src/protocols/scoring/methods/pcs2/PcsInputCenterManager.ccSingleton that hold everything about the input PCS This avoid multiple reading of the input file
src/protocols/scoring/methods/pcs2/PcsInputCenterManager.fwd.hhChristophe Schmitz
src/protocols/scoring/methods/pcs2/PcsInputCenterManager.hhSingleton that hold everything about the input PCS This avoid multiple reading of the input files
src/protocols/scoring/methods/pcs2/PcsInputFile.ccRead all input from a .npc input file, and hold the data in the class One file per lanthanide data
src/protocols/scoring/methods/pcs2/PcsInputFile.fwd.hhRead all input from a .npc input file, and hold the data in the class
src/protocols/scoring/methods/pcs2/PcsInputFile.hhRead all input from a .npc input file, and hold the data in the class. One file per lanthanide data
src/protocols/scoring/methods/pcs2/PcsInputLine.cc
src/protocols/scoring/methods/pcs2/PcsInputLine.fwd.hhClass that hold a line data of the input file
src/protocols/scoring/methods/pcs2/PcsInputLine.hhClass that hold a line data of the input file
src/protocols/scoring/methods/pcs2/PcsTensor.ccHold chi-tensor information of PCS
src/protocols/scoring/methods/pcs2/PcsTensor.fwd.hh
src/protocols/scoring/methods/pcs2/PcsTensor.hhHold chi-tensor information of PCS
src/protocols/scoring/methods/pcs2/TensorsOptimizer.cc
src/protocols/scoring/methods/pcs2/TensorsOptimizer.fwd.hh
src/protocols/scoring/methods/pcs2/TensorsOptimizer.hh
src/protocols/scoring/methods/pcs2/TensorsOptimizerFix.cc
src/protocols/scoring/methods/pcs2/TensorsOptimizerFix.fwd.hh
src/protocols/scoring/methods/pcs2/TensorsOptimizerFix.hh
src/protocols/scoring/methods/pcs2/TensorsOptimizerSvd.cc
src/protocols/scoring/methods/pcs2/TensorsOptimizerSvd.fwd.hh
src/protocols/scoring/methods/pcs2/TensorsOptimizerSvd.hh
src/protocols/scoring/methods/saxs/PDDFEnergy.cc
src/protocols/scoring/methods/saxs/PDDFEnergy.fwd.hhForward declaration of a PDDF energy term
src/protocols/scoring/methods/saxs/PDDFEnergy.hh
src/protocols/scoring/methods/saxs/PDDFEnergyCreator.hhDeclaration for the class that connects PDDFEnergyCreator with the ScoringManager
src/protocols/seeded_abinitio/CAcstGenerator.cc
src/protocols/seeded_abinitio/CAcstGenerator.hh
src/protocols/seeded_abinitio/CAcstGeneratorCreator.hh
src/protocols/seeded_abinitio/CloseFold.cc
src/protocols/seeded_abinitio/CloseFold.hh
src/protocols/seeded_abinitio/CloseFoldCreator.hh
src/protocols/seeded_abinitio/CoordinateCst.ccAllows to add coordinate constraints to the pose based on parsed spans or residues residues specified are parsed at runtime not at parse time, so it can be used somewhat used with length changes currently it only adds CA constraints, but hopefully at some time point others too
src/protocols/seeded_abinitio/CoordinateCst.hh
src/protocols/seeded_abinitio/CoordinateCstCreator.hh
src/protocols/seeded_abinitio/DefineMovableLoops.cc
src/protocols/seeded_abinitio/DefineMovableLoops.hh
src/protocols/seeded_abinitio/DefineMovableLoopsCreator.hh
src/protocols/seeded_abinitio/GrowPeptides.ccDifferent ways of growing peptide sequences
src/protocols/seeded_abinitio/GrowPeptides.hh
src/protocols/seeded_abinitio/GrowPeptidesCreator.hh
src/protocols/seeded_abinitio/SeededAbinitio_util.cc
src/protocols/seeded_abinitio/SeededAbinitio_util.hh
src/protocols/seeded_abinitio/SeedFoldTree.cc
src/protocols/seeded_abinitio/SeedFoldTree.fwd.hh
src/protocols/seeded_abinitio/SeedFoldTree.hh
src/protocols/seeded_abinitio/SeedFoldTreeCreator.hh
src/protocols/seeded_abinitio/SeedSetupMover.ccMover to set up packer task and movemap for seededabinitio
src/protocols/seeded_abinitio/SeedSetupMover.hh
src/protocols/seeded_abinitio/SeedSetupMoverCreator.hh
src/protocols/seeded_abinitio/SwapSegment.cc
src/protocols/seeded_abinitio/SwapSegment.hh
src/protocols/seeded_abinitio/SwapSegmentCreator.hh
src/protocols/simple_filters/AbinitioBaseFilter.cc
src/protocols/simple_filters/AbinitioBaseFilter.hhHeader file for AbinitioBaseFilter.cc
src/protocols/simple_filters/AlaScan.cc
src/protocols/simple_filters/AlaScan.fwd.hh
src/protocols/simple_filters/AlaScan.hhDefinition of filter class AlsScan
src/protocols/simple_filters/AlaScanCreator.hhFilterCreators for the AlaScanCreator
src/protocols/simple_filters/AtomicContactFilter.cc
src/protocols/simple_filters/AtomicContactFilter.hh
src/protocols/simple_filters/AtomicContactFilterCreator.hhFilterCreator for the AtomicContactFilter
src/protocols/simple_filters/AtomicDistanceFilter.cc
src/protocols/simple_filters/AtomicDistanceFilter.hhFilter for looking at specific atom distances
src/protocols/simple_filters/AtomicDistanceFilterCreator.hhFilterCreator for the AtomicDistanceFilter
src/protocols/simple_filters/BatchNrEvaluator.cc
src/protocols/simple_filters/BatchNrEvaluator.hh
src/protocols/simple_filters/BuriedUnsatHbondFilter.cc
src/protocols/simple_filters/BuriedUnsatHbondFilter.fwd.hh
src/protocols/simple_filters/BuriedUnsatHbondFilter.hhDefinition of filter class BuriedUnsatHbondFilter
src/protocols/simple_filters/BuriedUnsatHbondFilterCreator.hhFilterCreators for the BuriedUnsatHbondFilterCreator
src/protocols/simple_filters/CamShiftEvaluator.cc
src/protocols/simple_filters/CamShiftEvaluator.hh
src/protocols/simple_filters/CamShiftEvaluatorCreator.cc
src/protocols/simple_filters/CamShiftEvaluatorCreator.hhHeader for CamShiftEvaluatorCreator
src/protocols/simple_filters/ChiWellRmsdEvaluator.cc
src/protocols/simple_filters/ChiWellRmsdEvaluator.hh
src/protocols/simple_filters/ChiWellRmsdEvaluatorCreator.cc
src/protocols/simple_filters/ChiWellRmsdEvaluatorCreator.hhHeader for ChiWellRmsdEvaluatorCreator
src/protocols/simple_filters/ClashEvaluator.cc
src/protocols/simple_filters/ClashEvaluator.hh
src/protocols/simple_filters/COFilter.ccRuns reject or accept filters on pose
src/protocols/simple_filters/COFilter.hh
src/protocols/simple_filters/ConservedPosMutationFilter.cc
src/protocols/simple_filters/ConservedPosMutationFilter.fwd.hh
src/protocols/simple_filters/ConservedPosMutationFilter.hhHeader file for ConservedPosMutationFitler class
src/protocols/simple_filters/ConservedPosMutationFilterCreator.hhFilterCreator for the ConservedPosMutationFilter
src/protocols/simple_filters/ContactMapEvaluator.cc
src/protocols/simple_filters/ContactMapEvaluator.hh
src/protocols/simple_filters/ContactMapEvaluatorCreator.cc
src/protocols/simple_filters/ContactMapEvaluatorCreator.hhHeader for ContactMapEvaluatorCreator
src/protocols/simple_filters/DdgFilter.cc
src/protocols/simple_filters/DdgFilter.fwd.hh
src/protocols/simple_filters/DdgFilter.hhDefinition of filter class DdgFilter
src/protocols/simple_filters/DdgFilterCreator.hhFilterCreators for the DdgFilterCreator
src/protocols/simple_filters/EnergyPerResidueFilter.cc
src/protocols/simple_filters/EnergyPerResidueFilter.fwd.hh
src/protocols/simple_filters/EnergyPerResidueFilter.hhDefinition of filter class EnergyPerResidueFilter
src/protocols/simple_filters/EnergyPerResidueFilterCreator.hhFilterCreators for the EnergyPerResidueFilterCreator
src/protocols/simple_filters/EvaluatedTrialMover.cc
src/protocols/simple_filters/EvaluatedTrialMover.hh
src/protocols/simple_filters/ExternalEvaluator.cc
src/protocols/simple_filters/ExternalEvaluator.hh
src/protocols/simple_filters/ExtraScoreEvaluatorCreator.cc
src/protocols/simple_filters/ExtraScoreEvaluatorCreator.hhHeader for ExtraScoreEvaluatorCreator
src/protocols/simple_filters/HolesFilter.cc
src/protocols/simple_filters/HolesFilter.fwd.hhFilter structures by will's hole score
src/protocols/simple_filters/HolesFilter.hhHeader file for HolesFilter class
src/protocols/simple_filters/HolesFilterCreator.hhFilterCreator for the HolesFilter
src/protocols/simple_filters/InterfaceSasaFilter.cc
src/protocols/simple_filters/InterfaceSasaFilter.fwd.hh
src/protocols/simple_filters/InterfaceSasaFilter.hhDefinition of filter class InterfaceSasaFilter
src/protocols/simple_filters/InterfaceSasaFilterCreator.hhFilterCreators for the InterfaceSasaFilterCreator
src/protocols/simple_filters/JScoreEvaluator.cc
src/protocols/simple_filters/JScoreEvaluator.hh
src/protocols/simple_filters/JScoreEvaluatorCreator.cc
src/protocols/simple_filters/JScoreEvaluatorCreator.hhHeader for JScoreEvaluatorCreator
src/protocols/simple